Compositions and methods for treating chemotherapy resistant cancer

ABSTRACT

The present invention features methods for increasing sensitivity and/or reversing resistance to chemotherapy, methods for treating or preventing a cancer in a subject, methods for treating clonal hematopoiesis of indeterminate potential in a subject, and methods of identifying resistance or sensitivity to chemotherapy in a subject. In some embodiments, the methods contain the step of administering an agent that inhibits the expression or activity of a Protein phosphatase 1D (PPM1D) polypeptide or polynucleotide. The present invention also features compositions for increasing sensitivity and/or reversing resistance to chemotherapy.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority to and the benefit of U.S. Provisional Application No. 62/306,952 filed Mar. 11, 2016, the disclosure of which is incorporated herein by reference in its entirety.

STATEMENT OF RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSORED RESEARCH

This invention was made with government support under Grant No. P01 CA066996 awarded by the National Institutes of Health. The government has certain rights in the invention.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Jul. 29, 2020, is named 167741_010402_US_SL.txt and is 102,996 bytes in size.

BACKGROUND OF THE INVENTION

Cancer remains a global health problem. A common treatment for patients with cancer is chemotherapy. However, patients receiving chemotherapy often develop resistance to the chemotherapy. New, improved methods of treating cancer in patients, particularly patients who have developed resistance to chemotherapy, are urgently needed.

SUMMARY OF THE INVENTION

As described below, the present invention features compositions and methods that are useful for treating a cancer in a subject, particularly a subject that is resistant to chemotherapy and/or has mutations in Protein phosphatase 1D (PPM1D). The present invention also features compositions and methods that are useful for treating clonal hematopoiesis (e.g., clonal hematopoiesis of indeterminate potential (CHIP)) in a subject, particularly a subject that has mutations in PPM1D.

In one aspect, the invention provides a pharmaceutical composition containing an effective amount of an agent that inhibits the expression or activity of a PPM1D polynucleotide or polypeptide, in a pharmaceutically acceptable carrier. In various embodiments, the agent that inhibits the expression or activity of PPM1D polynucleotide or polypeptide is a small molecule PPM1D inhibitor or an inhibitory polynucleotide that reduces PPM1D expression.

In some embodiments, the pharmaceutical composition further contains a chemotherapeutic agent. In some other embodiments, the chemotherapeutic agent is a DNA damaging agent. In still other embodiments, the chemotherapeutic agent is Cytarabine, Doxorubicin, Cyclophosphamide, or Cisplatin. In some embodiments, the small molecule PPM1D inhibitor is GSK2830371, CCT007093, or an analog thereof.

In some embodiments, the small molecule PPM1D inhibitor inhibits activity of a PPM1D polypeptide comprising a truncation mutation and/or a gain-of-function mutation.

In another aspect, the invention provides a method of increasing sensitivity or reversing resistance of a cancer cell to a chemotherapeutic agent. The method contains the step of contacting the cell with an effective amount of a PPM1D inhibitor, an agent that inhibits the expression or activity of PPM1D polypeptide or polynucleotide, thereby increasing sensitivity of the cell the chemotherapeutic agent.

In yet another aspect, the invention provides a method of inhibiting proliferation of a cancer cell, the method containing the step of contacting the cell with an effective amount of a PPM1D inhibitor and contacting the cell with an effective amount of a chemotherapeutic agent, thereby inhibiting proliferation of the cell.

In another aspect, the invention provides a method of treating or preventing clonal hematopoiesis of indeterminate potential (CHIP) or a therapy-related myeloid neoplasm in a subject, the method involving administering a PPM1D inhibitor to a subject identified as having or having a propensity to develop CHIP or a therapy-related myeloid neoplasm.

In still another aspect, the invention provides a method of increasing sensitivity or reversing resistance to a chemotherapeutic agent in a subject having a cancer. The method contains the step of administering to the subject an effective amount of a PPM1D inhibitor, thereby increasing sensitivity or reversing resistance to the chemotherapeutic agent in the subject having a cancer.

In another aspect, the invention provides a method of treating a cancer in a subject. The method contains the step of administering to the subject an effective amount of a PPM1D inhibitor and administering to the subject an effective amount of a chemotherapeutic agent, thereby treating the cancer in the subject.

In another aspect, the invention provides a method of treating a cancer in a pre-identified subject, the method containing the step of administering to the subject an effective amount of a PPM1D inhibitor and an effective amount of a chemotherapeutic agent, where the subject is pre-identified as having a mutation in a PPM1D polynucleotide or polypeptide relative to a reference in a biological sample obtained from the subject.

In yet another aspect, the invention provides a method of treating clonal hematopoiesis of indeterminate potential in a pre-identified subject, the method containing the step of administering to the subject an effective amount of a PPM1D inhibitor, where the subject is pre-identified as having a mutation in a PPM1D polynucleotide or polypeptide relative to a reference in a biological sample obtained from the subject.

In various embodiments of any one of the aspects delineated herein, the subject is resistant to a chemotherapeutic agent. In some embodiments, the cell or the subject contains a mutation in a PPM1D polynucleotide or polypeptide. In some other embodiments, the mutation is a truncation mutation and/or a gain-of-function mutation.

In some embodiments, the cell is in vivo or in vitro. In some other embodiments, the agent that inhibits the expression or activity of PPM1D polypeptide or polynucleotide is one or more of small molecule PPM1D inhibitors GSK2830371 CCT007093, and analogs thereof. In some embodiments, the chemotherapeutic agent is any one of DNA damaging agents Cytarabine, Doxorubicin, Cyclophosphamide, and Cisplatin. In still other embodiments, the small molecule PPM1D inhibitor inhibits activity of a PPM1D polypeptide comprising a truncation mutation and/or a gain-of-function mutation.

In various embodiments of any one of the aspects delineated herein, the subject is human or murine. In various embodiments, the cell is a blood cell. In some embodiments, the cancer is a hematologic cancer. In some embodiments, the cancer is a therapy-related myeloid neoplasm. In still other embodiments, the biological sample is a blood, bone marrow, or tumor sample. In various embodiments of any one of the aspects delineated herein, the treatment selectively targets cells comprising a PPM1D mutation. In some embodiments, the propensity to develop CHIP is associated with chemotherapy.

In one aspect, the invention provides a kit containing a capture reagent specifically binding a PPM1D polynucleotide or polypeptide and an agent that inhibits the expression or activity of a PPM1D polynucleotide or polypeptide.

In another aspect, the invention provides a kit containing a capture reagent specifically binding a PPM1D polynucleotide or polypeptide and at least one agent selected from the group consisting of an agent that inhibits the expression or activity of a PPM1D polynucleotide or polypeptide and a chemotherapeutic agent. In some embodiments, the agent that inhibits the expression or activity of a PPM1D polynucleotide or polypeptide is one or more of PPM1D small molecule inhibitor such as GSK2830371, CCT007093, and analogs thereof. In some other embodiments, the chemotherapeutic agent is any one of DNA damaging agents Cytarabine, Doxorubicin, Cyclophosphamide and Cisplatin. In some embodiments, the capture reagent is a probe or primer.

Compositions and articles defined by the invention were isolated or otherwise manufactured in connection with the examples provided below. Other features and advantages of the invention will be apparent from the detailed description, and from the claims.

Definitions

Unless defined otherwise, all technical and scientific terms used herein have the meaning commonly understood by a person of ordinary skill in the art to which this invention belongs. The following references provide one of skill with a general definition of many of the terms used in this invention: Singleton et al., Dictionary of Microbiology and Molecular Biology (2nd ed. 1994); The Cambridge Dictionary of Science and Technology (Walker ed., 1988); The Glossary of Genetics, 5th Ed., R. Rieger et al. (eds.), Springer Verlag (1991); and Hale & Marham, The Harper Collins Dictionary of Biology (1991). As used herein, the following terms have the meanings ascribed to them below, unless specified otherwise.

By “agent” is meant any small molecule chemical compound, antibody, nucleic acid molecule, or polypeptide, or fragments thereof.

By “ameliorate” is meant decrease, suppress, attenuate, diminish, arrest, or stabilize the development or progression of a disease.

By “alteration” is meant a change (increase or decrease) in the expression levels or activity of a gene or polypeptide as detected by standard art known methods such as those described herein. As used herein, an alteration includes a 10% change in expression levels, a 25% change, a 40% change, and a 50% or greater change in expression levels.

By “analog” is meant a molecule that is not identical, but has analogous functional or structural features. For example, an analog of an agent of the invention (e.g., GSK2830371, CCT007093) retains the biological activity of the corresponding agent, while having certain chemical modifications that enhance the analog's function relative to the corresponding agent. Such modifications could increase the analog's protease resistance, membrane permeability, or half-life, without altering, for example, ligand binding.

“Biological sample” as used herein means a biological material isolated from a subject, including any tissue, cell, fluid, or other material obtained or derived from the subject. In some embodiments, the subject is human. The biological sample may contain any biological material suitable for detecting the desired analytes, and may comprise cellular and/or non-cellular material obtained from the subject. Biological samples include tissue samples (e.g., cell samples, biopsy samples). Biological samples also include bodily fluids, including, but not limited to, blood, blood serum, plasma, saliva, and urine. In particular embodiments, the biological sample is blood. In some embodiments, the biological sample is a blood, bone marrow, or tumor sample.

By “chemotherapeutic agent” is meant an agent having anti-neoplastic activity. In some embodiments, the chemotherapeutic agent is a DNA damaging agent. In certain embodiments, the chemotherapeutic agent is Cytarabine, Doxorubicin, Cyclophosphamide, or Cisplatin.

In some embodiments, the chemotherapeutic agent contains platinum. Examples of such an agent include, without limitation, cisplatin, carboplatin, and oxaliplatin. In some other embodiments, the chemotherapeutic agent is an anthracycline. Examples of anthracyclines include, without limitation, doxorubicin, daunorubicin, and idarubicin. In still other embodiments, the chemotherapeutic agent is an alkylating agent. Examples of alkylating agents include, without limitation, cyclophosphamide, melphalan, chlorambucil, and busulfan. In some embodiments, the chemotherapeutic agent is an antimetabolite. Exemplary antimetabolites include, without limitation, cytarabine, 5-fluorouracil, methotrexate, azathiopurine, 6-mercaptopurine, 6-thioguanine, and fludarabine.

By “clonal hematopoiesis of indeterminate potential (CHIP)” is meant a clonal somatic mutation in the bone marrow or blood, that may increase the risk of a hematological malignancy. In various embodiments, clonal hematopoiesis of indeterminate potential does not display diagnostic criteria for a hematologic malignancy. In various embodiments, there is an absence of definitive morphological evidence of a hematological neoplasm. In certain embodiments, the somatic mutation associated with hematological neoplasia is in one or more of PPM1D, TP53, DNMT3A, TET2, JAK2, SF3B1, ASXL1, CBL, GNB1, BCOR, U2AF1, CREBBP, CUX1, SRSF2, MLL2, SETD2, SETDB1, GNAS, BCORL1). In some embodiments, progression to overt neoplasia is approximately 0.5-1%.

In this disclosure, “comprises,” “comprising,” “containing” and “having” and the like can have the meaning ascribed to them in U.S. Patent law and can mean “includes,” “including,” and the like; “consisting essentially of” or “consists essentially” likewise has the meaning ascribed in U.S. Patent law and the term is open-ended, allowing for the presence of more than that which is recited so long as basic or novel characteristics of that which is recited is not changed by the presence of more than that which is recited, but excludes prior art embodiments.

By “CCT007093” or “CAS 1087-07-6” is meant a small molecule inhibitor having the following structure:

In some embodiments, CCT007093 is a small molecule PPM1D inhibitor.

By “Cisplatin” is meant a chemotherapeutic agent having the following structure:

In some embodiments, Cisplatin inhibits DNA replication by reacting with DNA to form intra- and interstrand crosslinks.

By “Cytarabine” is meant a chemotherapeutic agent having the following structure:

In some embodiments, Cytarabine inhibits synthesis of DNA.

By “Cyclophosphamide” is meant a chemotherapeutic agent having the following structure:

In some embodiments, Cyclophosphamide adds an alkyl group to DNA and inhibits DNA replication by forming intra- and interstrand DNA crosslinks.

“Detect” refers to identifying the presence, absence or amount of the analyte to be detected. In some embodiments, a PPM1D polypeptide or polynucleotide comprising a mutation is detected. In some embodiments, the mutation is a truncation mutation. In some embodiments, the mutation is a frameshift mutation that results in expression of a truncated PPM1D polypeptide relative to a wild-type PPM1D polypeptide.

By “detectable label” is meant a composition that when linked to a molecule of interest renders the latter detectable, via spectroscopic, photochemical, biochemical, immunochemical, or chemical means. For example, useful labels include radioactive isotopes, magnetic beads, metallic beads, colloidal particles, fluorescent dyes, electron-dense reagents, enzymes (for example, as commonly used in an ELISA), biotin, digoxigenin, or haptens.

By “disease” is meant any condition or disorder that damages or interferes with the normal function of a cell, tissue, or organ. Examples of diseases include cancer. In some embodiments, the cancer is a blood cancer. In some other embodiments, the blood cancer is acute myeloid leukemia.

By “DNA damaging agent” is meant any agent that alters the structure of DNA and/or inhibits DNA replication or DNA synthesis in a cell or in vitro. In some embodiments, the DNA damaging agent is Cytarabine, Doxorubicin, Cyclophosphamide, or Cisplatin.

By “Doxorubicin” is meant a chemotherapeutic agent having the following structure:

In some embodiments, Doxorubicin inhibits DNA replication.

By “effective amount” is meant the amount of a required to ameliorate the symptoms of a disease relative to an untreated patient. The effective amount of active compound(s) used to practice the present invention for therapeutic treatment of a disease varies depending upon the manner of administration, the age, body weight, and general health of the subject. Ultimately, the attending physician or veterinarian will decide the appropriate amount and dosage regimen. Such amount is referred to as an “effective” amount.

By “fragment” is meant a portion of a polypeptide or nucleic acid molecule. This portion contains at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% of the entire length of the reference nucleic acid molecule or polypeptide. A fragment may contain 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100, 200, 300, 400, 500, 600, 700, 800, 900, or 1000 nucleotides or amino acids.

By “GSK2830371” is meant a small molecule inhibitor having the following structure:

In some embodiments, GSK2830371 is a small molecule PPM1D inhibitor.

“Hybridization” means hydrogen bonding, which may be Watson-Crick, Hoogsteen or reversed Hoogsteen hydrogen bonding, between complementary nucleobases. For example, adenine and thymine are complementary nucleobases that pair through the formation of hydrogen bonds.

By “inhibitory nucleic acid” or “inhibitory polynucleotide” is meant a double-stranded RNA, siRNA, shRNA, or antisense RNA, or a portion thereof, or a mimetic thereof, that when administered to a mammalian cell results in a decrease (e.g., by 10%, 25%, 50%, 75%, or even 90-100%) in the expression of a target gene. Typically, a nucleic acid inhibitor comprises at least a portion of a target nucleic acid molecule, or an ortholog thereof, or comprises at least a portion of the complementary strand of a target nucleic acid molecule. For example, an inhibitory nucleic acid molecule comprises at least a portion of any or all of the nucleic acids delineated herein.

The terms “isolated,” “purified,” or “biologically pure” refer to material that is free to varying degrees from components which normally accompany it as found in its native state. “Isolate” denotes a degree of separation from original source or surroundings. “Purify” denotes a degree of separation that is higher than isolation. A “purified” or “biologically pure” protein is sufficiently free of other materials such that any impurities do not materially affect the biological properties of the protein or cause other adverse consequences. That is, a nucleic acid or peptide of this invention is purified if it is substantially free of cellular material, viral material, or culture medium when produced by recombinant DNA techniques, or chemical precursors or other chemicals when chemically synthesized. Purity and homogeneity are typically determined using analytical chemistry techniques, for example, polyacrylamide gel electrophoresis or high performance liquid chromatography. The term “purified” can denote that a nucleic acid or protein gives rise to essentially one band in an electrophoretic gel. For a protein that can be subjected to modifications, for example, phosphorylation or glycosylation, different modifications may give rise to different isolated proteins, which can be separately purified.

By “isolated polynucleotide” is meant a nucleic acid (e.g., a DNA) that is free of the genes which, in the naturally-occurring genome of the organism from which the nucleic acid molecule of the invention is derived, flank the gene. The term therefore includes, for example, a recombinant DNA that is incorporated into a vector; into an autonomously replicating plasmid or virus; or into the genomic DNA of a prokaryote or eukaryote; or that exists as a separate molecule (for example, a cDNA or a genomic or cDNA fragment produced by PCR or restriction endonuclease digestion) independent of other sequences. In addition, the term includes an RNA molecule that is transcribed from a DNA molecule, as well as a recombinant DNA that is part of a hybrid gene encoding additional polypeptide sequence.

By an “isolated polypeptide” is meant a polypeptide of the invention that has been separated from components that naturally accompany it. Typically, the polypeptide is isolated when it is at least 60%, by weight, free from the proteins and naturally-occurring organic molecules with which it is naturally associated. The preparation can be at least 75%, at least 90%, and at least 99%, by weight, a polypeptide of the invention. An isolated polypeptide of the invention may be obtained, for example, by extraction from a natural source, by expression of a recombinant nucleic acid encoding such a polypeptide; or by chemically synthesizing the protein. Purity can be measured by any appropriate method, for example, column chromatography, polyacrylamide gel electrophoresis, or by HPLC analysis.

By “marker” is meant any protein or polynucleotide having an alteration in expression level or activity that is associated with a disease or disorder.

By “mutation” is meant a change in a polypeptide or polynucleotide sequence relative to a reference sequence. In some embodiments, the reference sequence is a wild-type sequence. Exemplary mutations include point mutations, missense mutations, amino acid substitutions, and frameshift mutations. As used herein, a “truncation mutation” is a mutation that results in expression of a polypeptide having a decreased number of amino acid residues relative to the wild-type polypeptide. A “loss-of-function mutation” is a mutation that decreases or abolishes an activity or function of a polypeptide. A “gain-of-function mutation” is a mutation that enhances or increases an activity or function of a polypeptide. In some embodiments, the PPM1D mutation is a truncation mutation. In some embodiments, the PPM1D truncation mutation is a gain-of-function mutation.

As used herein, “obtaining” as in “obtaining an agent” includes synthesizing, purchasing, or otherwise acquiring the agent.

By “Protein phosphatase 1D (PPM1D) polypeptide” is meant a polypeptide or fragment thereof having at least about 85% amino acid identity to NCBI Accession No. NP_003611.1 and having phosphatase activity. The sequence at NCBI Accession No. NP_003611.1 is shown below:

(SEQ ID NO: 1)   1 maglyslgvs vfsdqggrky medvtqivve peptaeekps prrslsqplp prpspaalpg  61 gevsgkgpav aareardplp dagaspapsr ccrrrssvaf favcdghggr eaaqfarehl 121 wgfikkqkgf tssepakvca airkgflach lamwkklaew pktmtglpst sgttasvvii 181 rgmkmyvahv gdsgvvlgiq ddpkddfvra vevtqdhkpe lpkererieg lggsvmnksg 241 vnrvvwkrpr lthngpvrrs tvidqipfla varalgdlws ydffsgefvv spepdtsvht 301 ldpqkhkyii lgsdglwnmi ppgdaismcq dqeekkylmg ehggscakml vnralgrwrq 361 rmlradntsa ivicispevd nqgnftnede lylnitdsps ynsqetcvmt pspcstppvk 421 sleedpwprv nskdhipalv rsnafsenfl evsaeiaren vqgvvipskd pepleencak 481 altlrihdsl nnslpiglvp tnstntvmdq knlkmstpgq mkaqeiertp ptnfkrtlee 541 snsgplmkkh rrnglsrssg aqpaslptts qrknsvkltm rrrlrgqkki gnpllhqhrk 601 tvcvc

By “Protein phosphatase 1D (PPM1D) polynucleotide” is meant a polynucleotide encoding a PPM1D polypeptide. An exemplary PPM1D polynucleotide sequence is provided at NCBI Accession No. NM_003620.3. The sequence is provided below:

(SEQ ID NO: 2)    1 ggggaagcgc agtgcgcagg cgcaactgcc tggctctgct cgctccggcg ctccggccca   61 gctctcgcgg acaagtccag acatcgcgcg cccccccttc tccgggtccg ccccctcccc  121 cttctcggcg tcgtcgaaga taaacaatag ttggccggcg agcgcctagt gtgtctcccg  181 ccgccggatt cggcgggctg cgtgggaccg gcgggatccc ggccagccgg ccatggcggg  241 gctgtactcg ctgggagtga gcgtcttctc cgaccagggc gggaggaagt acatggagga  301 cgttactcaa atcgttgtgg agcccgaacc gacggctgaa gaaaagccct cgccgcggcg  361 gtcgctgtct cagccgttgc ctccgcggcc gtcgccggcc gcccttcccg gcggcgaagt  421 ctcggggaaa ggcccagcgg tggcagcccg agaggctcgc gaccctctcc cggacgccgg  481 ggcctcgccg gcacctagcc gctgctgccg ccgccgttcc tccgtggcct ttttcgccgt  541 gtgcgacggg cacggcgggc gggaggcggc acagtttgcc cgggagcact tgtggggttt  601 catcaagaag cagaagggtt tcacctcgtc cgagccggct aaggtttgcg ctgccatccg  661 caaaggcttt ctcgcttgtc accttgccat gtggaagaaa ctggcggaat ggccaaagac  721 tatgacgggt cttcctagca catcagggac aactgccagt gtggtcatca ttcggggcat  781 gaagatgtat gtagctcacg taggtgactc aggggtggtt cttggaattc aggatgaccc  841 gaaggatgac tttgtcagag ctgtggaggt gacacaggac cataagccag aacttcccaa  901 ggaaagagaa cgaatcgaag gacttggtgg gagtgtaatg aacaagtctg gggtgaatcg  961 tgtagtttgg aaacgacctc gactcactca caatggacct gttagaagga gcacagttat 1021 tgaccagatt ccttttctgg cagtagcaag agcacttggt gatttgtgga gctatgattt 1081 cttcagtggt gaatttgtgg tgtcacctga accagacaca agtgtccaca ctcttgaccc 1141 tcagaagcac aagtatatta tattggggag tgatggactt tggaatatga ttccaccaca 1201 agatgccatc tcaatgtgcc aggaccaaga ggagaaaaaa tacctgatgg gtgagcatgg 1261 acaatcttgt gccaaaatgc ttgtgaatcg agcattgggc cgctggaggc agcgtatgct 1321 ccgagcagat aacactagtg ccatagtaat ctgcatctct ccagaagtgg acaatcaggg 1381 aaactttacc aatgaagatg agttatacct gaacctgact gacagccctt cctataatag 1441 tcaagaaacc tgtgtgatga ctccttcccc atgttctaca ccaccagtca agtcactgga 1501 ggaggatcca tggccaaggg tgaattctaa ggaccatata cctgccctgg ttcgtagcaa 1561 tgccttctca gagaattttt tagaggtttc agctgagata gctcgagaga atgtccaagg 1621 tgtagtcata ccctcaaaag atccagaacc acttgaagaa aattgcgcta aagccctgac 1681 tttaaggata catgattctt tgaataatag ccttccaatt ggccttgtgc ctactaattc 1741 aacaaacact gtcatggacc aaaaaaattt gaagatgtca actcctggcc aaatgaaagc 1801 ccaagaaatt gaaagaaccc ctccaacaaa ctttaaaagg acattagaag agtccaattc 1861 tggccccctg atgaagaagc atagacgaaa tggcttaagt cgaagtagtg gtgctcagcc 1921 tgcaagtctc cccacaacct cacagcgaaa gaactctgtt aaactcacca tgcgacgcag 1981 acttaggggc cagaagaaaa ttggaaatcc tttacttcat caacacagga aaactgtttg 2041 tgtttgctga aatgcatctg ggaaatgagg tttttccaaa cttaggatat aagagggctt 2101 tttaaatttg gtgccgatgt tgaacttttt ttaaggggag aaaattaaaa gaaatataca 2161 gtttgacttt ttggaattca gcagttttat cctggccttg tacttgcttg tattgtaaat 2221 gtggattttg tagatgttag ggtataagtt gctgtaaaat ttgtgtaaat ttgtatccac 2281 acaaattcag tctctgaata cacagtattc agagtctctg atacacagta attgtgacaa 2341 tagggctaaa tgtttaaaga aatcaaaaga atctattaga ttttagaaaa acatttaaac 2401 tttttaaaat acttattaaa aaatttgtat aagccacttg tcttgaaaac tgtgcaactt 2461 tttaaagtaa attattaagc agactggaaa agtgatgtat tttcatagtg acctgtgttt 2521 cacttaatgt ttcttagagc caagtgtctt ttaaacatta ttttttattt ctgatttcat 2581 aattcagaac taaatttttc atagaagtgt tgagccatgc tacagttagt cttgtcccaa 2641 ttaaaatact atgcagtatc tcttacatca gtagcatttt tctaaaacct tagtcatcag 2701 atatgcttac taaatcttca gcatagaagg aagtgtgttt gcctaaaaca atctaaaaca 2761 attcccttct ttttcatccc agaccaatgg cattattagg tcttaaagta gttactccct 2821 tctcgtgttt gcttaaaata tgtgaagttt tccttgctat ttcaataaca gatggtgctg 2881 ctaattccca acatttctta aattatttta tatcatacag ttttcattga ttatatgggt 2941 atatattcat ctaataaatc agtgaactgt tcctcatgtt gctgaatttg tagttgttgg 3001 tttattttaa tggtatgtac aagttgagta tcccttatcc aaaatgcttg ggaccagaag 3061 tgtttcagat tttttaaaat tttggaatat ttgctttata ctgagctttt gagtgttccc 3121 aatctgaaat tcaaaatgct ctaatgagca tttcctttga gcatcatgcc tgctctgaaa 3181 aagtttctga ttctggagca ttttggattt tggattttca gattagggat gcttaacctg 3241 gattaacatt ctgttgtgcc atgatcatgc tttacagtga gtgtatttta tttatttatt 3301 attttgtttg tttgtttgag atggagtctc actctgtcat ccaggctaga gtgcagtggc 3361 gtgatctcgg ctgactgcaa cctctgcctc ccgggttcaa gtgattctcc tgcctcaatc 3421 tctctcccca gaagctggga ttacaggtgt gtgccaccac acccggctaa tttttttttt 3481 tttttttgag atggagtcta gctctgtcat ccaggctgga gtgcagtggt gtgatctcgg 3541 ctccctgcaa cctctgcctt ctgggttcct gcgattctcc tgcctcagcc tcctgagtag 3601 ctgagattac aggcacgcgc cactgtgccc agccaatttt tgtattttta gtagagatgg 3661 ggtttcacat gtcagtcatg ctggtcttga tctcctgacc tcgtgatcca cccgcctcga 3721 cctcccaaag tactgggatt acaggcgtga gccaccgcat ccggcctgag ttttatgctt 3781 tcaatgtatt tcttacattt cagttcaagt gattttcatg tctcagcctc ctgagtagct 3841 ggaactacag gtgcgtgcca ccatgcctgg ctaagttttg tatttttagt agagatgggt 3901 tttcatcatg ttggccaaga tggtcttgat ctcttgacct catgatccac cagcctaggc 3961 ctcccaaagt gctgggatta caggtgtgag ccaccgtgcc cagccaacta tgccattatt 4021 taaccatgtc cacacattct ggttattttc aatattttgc agaagataat tcttgatcgg 4081 tgtgtcttat gccacaagga ttaaaatatg tattcattgc tacaaaacaa tatctcgaaa 4141 tttagcagtt taaaacaaca aatattatct ccagtttctg agcctcagaa atctgagagt 4201 ggtttagctg ggtgatagtc tcgtggtttt ggtcaagcta ccaaccaggg ctacaatctt 4261 tcgaaggtgt cattggggct agaagatctg cttcccgcaa gactcacagc tgttggcagg 4321 agacctcagt ttgttgccac atgttcccct ccagagggcc tctcacaaca tggcagttat 4381 ttgtccccag agcaagcaac accggagggc aaggaagaag ccatgatgtt ttttgtaacc 4441 tagcctctga aagtgtcata ccaattctgt attttgttgg tcacacagac caagtcaact 4501 acaacgtggg agactcctac acaaggcatg aattctagga ggtgggcatt tttaagtgtc 4561 atctggaagg aggctgtcac aacctggaag ttaaaagcat tgatattctg aaatacagcg 4621 tgtataacat tgttttagta gggtgtgcaa tagttatgtt ttggtaatag cattaatgaa 4681 caatgttatt ttcatcttcc agacatctgg aagattgctc tagtggagta aaacatctta 4741 atgtattttg tccctaaata aactatctca ctaacaaaaa aaaaaaaaaa

By “PPM1D inhibitor” is meant an agent that reduces or eliminates a biological function or activity of a PPM1D polypeptide. Exemplary biological activities or functions of a PPM1D polypeptide include serine/threonine phosphatase activity, dephosphorylation of p53 and Chk1, and negative regulation of cell stress response. Examples of a PPM1D inhibitor include, without limitation, GSK2830371 and CCT007093. In particular embodiments, the PPM1D inhibitor is GSK2830371 or CCT007093. Other PPMID inhibitors are described in, for example, Belova, Demidov et al, Cancer Biology & Therapy 2005, October; 4(10):1154-8, and Yagi, Sakaguchi et al, Bioorganic & Medicinal Chemistry Letters 2012 Jan. 1; 22(1):729-32.

By “reduces” is meant a negative alteration of at least 10%, 25%, 50%, 75%, or 100%.

By “reference” is meant a standard or control condition.

A “reference sequence” is a defined sequence used as a basis for sequence comparison. A reference sequence may be a subset of or the entirety of a specified sequence; for example, a segment of a full-length cDNA or gene sequence, or the complete cDNA or gene sequence. In some embodiments, the reference sequence is a wild-type PPM1D polynucleotide or polypeptide sequence. For polypeptides, the length of the reference polypeptide sequence will generally be at least about 16 amino acids, at least about 20 amino acids, or at least about 25 amino acids. The length of the reference polypeptide sequence can be about 35 amino acids, about 50 amino acids, or about 100 amino acids. For nucleic acids, the length of the reference nucleic acid sequence will generally be at least about 50 nucleotides, at least about 60 nucleotides, or at least about 75 nucleotides. The length of the reference nucleic acid sequence can be about 100 nucleotides, about 300 nucleotides or any integer thereabout or therebetween.

By “siRNA” is meant a double stranded RNA. Optimally, an siRNA is 18, 19, 20, 21, 22, 23 or 24 nucleotides in length and has a 2 base overhang at its 3′ end. These dsRNAs can be introduced to an individual cell or to a whole animal; for example, they may be introduced systemically via the bloodstream. Such siRNAs are used to downregulate mRNA levels or promoter activity.

By “specifically binds” is meant a compound or antibody that recognizes and binds a polypeptide of the invention, but which does not substantially recognize and bind other molecules in a sample, for example, a biological sample, which naturally includes a polypeptide of the invention. In some embodiments, a capture reagent specifically binds a PPM1D polypeptide or polynucleotide. In some embodiments, the capture reagent that specifically binds a PPM1D polypeptide or polynucleotide is an antibody, a primer, or a probe.

Nucleic acid molecules useful in the methods of the invention include any nucleic acid molecule that encodes a polypeptide of the invention or a fragment thereof. Such nucleic acid molecules need not be 100% identical with an endogenous nucleic acid sequence, but will typically exhibit substantial identity. Polynucleotides having “substantial identity” to an endogenous sequence are typically capable of hybridizing with at least one strand of a double-stranded nucleic acid molecule. Nucleic acid molecules useful in the methods of the invention include any nucleic acid molecule that encodes a polypeptide of the invention or a fragment thereof. Such nucleic acid molecules need not be 100% identical with an endogenous nucleic acid sequence, but will typically exhibit substantial identity. Polynucleotides having “substantial identity” to an endogenous sequence are typically capable of hybridizing with at least one strand of a double-stranded nucleic acid molecule. By “hybridize” is meant pair to form a double-stranded molecule between complementary polynucleotide sequences (e.g., a gene described herein), or portions thereof, under various conditions of stringency. (See, e.g., Wahl, G. M. and S. L. Berger (1987) Methods Enzymol. 152:399; Kimmel, A. R. (1987) Methods Enzymol. 152:507).

For example, stringent salt concentration will ordinarily be less than about 750 mM NaCl and 75 mM trisodium citrate, less than about 500 mM NaCl and 50 mM trisodium citrate, or less than about 250 mM NaCl and 25 mM trisodium citrate. Low stringency hybridization can be obtained in the absence of organic solvent, e.g., formamide, while high stringency hybridization can be obtained in the presence of at least about 35% formamide, or at least about 50% formamide. Stringent temperature conditions will ordinarily include temperatures of at least about 30° C., at least about 37° C., and at least about 42° C. Varying additional parameters, such as hybridization time, the concentration of detergent, e.g., sodium dodecyl sulfate (SDS), and the inclusion or exclusion of carrier DNA, are well known to those of ordinary skill in the art. Various levels of stringency are accomplished by combining these various conditions as needed. In one embodiment, hybridization will occur at 30° C. in 750 mM NaCl, 75 mM trisodium citrate, and 1% SDS. In another embodiment, hybridization will occur at 37° C. in 500 mM NaCl, 50 mM trisodium citrate, 1% SDS, 35% formamide, and 100 μg/ml denatured salmon sperm DNA (ssDNA). In yet another embodiment, hybridization will occur at 42° C. in 250 mM NaCl, 25 mM trisodium citrate, 1% SDS, 50% formamide, and 200 μg/ml ssDNA. Useful variations on these conditions will be readily apparent to those of ordinary skill in the art.

For most applications, washing steps that follow hybridization will also vary in stringency. Wash stringency conditions can be defined by salt concentration and by temperature. As above, wash stringency can be increased by decreasing salt concentration or by increasing temperature. For example, stringent salt concentration for the wash steps will be less than about 30 mM NaCl and 3 mM trisodium citrate, or less than about 15 mM NaCl and 1.5 mM trisodium citrate. Stringent temperature conditions for the wash steps will ordinarily include a temperature of at least about 25° C., at least about 42° C., and at least about 68° C. In one embodiment, wash steps will occur at 25° C. in 30 mM NaCl, 3 mM trisodium citrate, and 0.1% SDS. In another embodiment, wash steps will occur at 42 C in 15 mM NaCl, 1.5 mM trisodium citrate, and 0.1% SDS. In yet another embodiment, wash steps will occur at 68° C. in 15 mM NaCl, 1.5 mM trisodium citrate, and 0.1% SDS. Additional variations on these conditions will be readily apparent to those of ordinary skill in the art. Hybridization techniques are well known to those of ordinary skill in the art and are described, for example, in Benton and Davis (Science 196:180, 1977); Grunstein and Hogness (Proc. Natl. Acad. Sci., USA 72:3961, 1975); Ausubel et al. (Current Protocols in Molecular Biology, Wiley Interscience, New York, 2001); Berger and Kimmel (Guide to Molecular Cloning Techniques, 1987, Academic Press, New York); and Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, New York.

By “substantially identical” is meant a polypeptide or nucleic acid molecule exhibiting at least 50% identity to a reference amino acid sequence (for example, any one of the amino acid sequences described herein) or nucleic acid sequence (for example, any one of the nucleic acid sequences described herein). Such a sequence is at least 60%, at least 80%, at least 85%, at least 90%, at least 95% or even at least 99% identical at the amino acid level or nucleic acid to the sequence used for comparison.

Sequence identity is typically measured using sequence analysis software (for example, Sequence Analysis Software Package of the Genetics Computer Group, University of Wisconsin Biotechnology Center, 1710 University Avenue, Madison, Wis. 53705, BLAST, BESTFIT, GAP, or PILEUP/PRETTYBOX programs). Such software matches identical or similar sequences by assigning degrees of homology to various substitutions, deletions, and/or other modifications. Conservative substitutions typically include substitutions within the following groups: glycine, alanine; valine, isoleucine, leucine; aspartic acid, glutamic acid, asparagine, glutamine; serine, threonine; lysine, arginine; and phenylalanine, tyrosine. In an exemplary approach to determining the degree of identity, a BLAST program may be used, with a probability score between e⁻³ and e⁻¹⁰⁰ indicating a closely related sequence.

By “subject” is meant a mammal, including, but not limited to, a human or non-human mammal, such as a bovine, equine, canine, ovine, mouse, rat, or feline. In some embodiments, the subject is a human.

Ranges provided herein are understood to be shorthand for all of the values within the range. For example, a range of 1 to 50 is understood to include any number, combination of numbers, or sub-range from the group consisting 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50.

As used herein, the terms “treat,” treating,” “treatment,” and the like refer to reducing or ameliorating a disorder and/or symptoms associated therewith. It will be appreciated that, although not precluded, treating a disorder or condition does not require that the disorder, condition or symptoms associated therewith be completely eliminated.

Unless specifically stated or obvious from context, as used herein, the term “or” is understood to be inclusive. Unless specifically stated or obvious from context, as used herein, the terms “a”, “an”, and “the” are understood to be singular or plural.

Unless specifically stated or obvious from context, as used herein, the term “about” is understood as within a range of normal tolerance in the art, for example within 2 standard deviations of the mean. About can be understood as within 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.5%, 0.1%, 0.05%, or 0.01% of the stated value. Unless otherwise clear from context, all numerical values provided herein are modified by the term about.

The recitation of a listing of chemical groups in any definition of a variable herein includes definitions of that variable as any single group or combination of listed groups. The recitation of an embodiment for a variable or aspect herein includes that embodiment as any single embodiment or in combination with any other embodiments or portions thereof.

Any compositions or methods provided herein can be combined with one or more of any of the other compositions and methods provided herein.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1E show that PPM1D mutations lead to chemotherapy resistance. FIG. 1A depicts a CRISPR-Cas9 system with an sgRNA targeting the last exon of hPPM1D, which was used to induce mutations in exon six of PPM1D. FIG. 1B provides immunoblots showing that mutations in the last exon of PPM1D result in truncation of the protein in subcloned and pooled Molm13 cells. FIG. 1C is a plot showing that mutations in PPM1D resulted in a resistance to treatment with Cytarabine. FIG. 1D is a plot showing that PPM1D mutant cells had a competitive advantage under the selective pressure of chemotherapy (Cytarabine) treatment. FIG. 1E is a plot showing that PPM1D mutations led to chemotherapy resistance. PPM1D mutant cells had a competitive advantage under the selective pressure of Cyclophosphamide treatment.

FIGS. 2A-2I show that truncating PPM1D mutations confer chemotherapy resistance. FIG. 2A is a map of the PPM1D gene showing the location of frame-shift and non-sense mutations in PPM1D identified in the blood cells of a cohort of 29,562 persons. FIG. 2B provides immunoblots of whole cell lysates from Molm13 control cells (control), PPM1D-mutant pooled clones and PPM1D frame-shift (fs) mutant single cell clones probed with anti-PPM1D and anti-Actin. FIG. 2C is a plot depicting viability assays in Molm13 PPM1D-mutant or control single cells clones that were treated with increasing concentrations of cytarabine for 72 hours. FIG. 2D is a plot depicting viability assays in Molm13 PPM1D-mutant or control single cells clones that were treated with increasing concentrations of cyclophosphamide for 72 hours. FIG. 2E is a plot depicting viability assays in Molm13 PPM1D-mutant or control single cells clones that were treated with increasing concentrations of cisplatin for 72 hours. FIG. 2F is a plot depicting flow cytometric readout of competition experiment with 5% pooled Molm13 PPM1D-mutant cells and 95% pooled Molm13 control cells exposed to 100 nM Cytarabine or vehicle for 24 days. FIG. 2G is a plot depicting flow cytometric readout of competition experiment with 5% pooled Molm13 PPM1D-mutant cells and 95% pooled Molm13 control cells exposed to 350 nM Cyclophosphamide or vehicle for 24 days. FIG. 2H is a plot depicting flow cytometric readout of competition experiment with 5% pooled Molm13 PPM1D-mutant cells and 95% pooled Molm13 control cells exposed to 1 μM Cisplatin or vehicle for 24 days. FIG. 2I is a plot depicting flow cytometric analysis of peripheral blood leukocytes in mice exposed to several rounds of cytarabine or vehicle treatment. PPM1D and control sgRNAs were identified through their fluorophores.

FIGS. 3A-3C show the sequencing read-out of an in vitro competition experiment. FIG. 3A is a plot depicting Next Generation Sequencing readout of cells collected on day 4 and 16 of in vitro competition experiment in which 5% pooled Molm13 PPM1D-mutant cells and 95% Molm13 control cells were mixed and exposed to 100 nM Cytarabine or vehicle. FIG. 3B is a plot depicting Next Generation Sequencing readout of cells collected on day 4 and 16 of in vitro competition experiment in which 5% pooled Molm13 PPM1D-mutant cells and 95% Molm13 control cells were mixed and exposed to 350 nM Cyclophosphamide or vehicle. FIG. 3C is a plot depicting Next Generation Sequencing readout of cells collected on day 4 and 16 of in vitro competition experiment in which 5% pooled Molm13 PPM1D-mutant cells and 95% Molm13 control cells were mixed and exposed to 1 μM Cisplatin or vehicle.

FIGS. 4A-4C show that PPM1D mutations led to increased serial replating potential and clonal dominance. FIG. 4A is a graph showing that PPM1D mutant cKIT positive cells had increased serial replating potential in vitro. FIG. 4B provides an in vivo experimental schema. cKIT positive cells from a Cas9^(+/−)VavCre⁺ mouse were infected with sgRNAs targeting mPPM1D or non-coding region of the genome (control). Eight hours after lentiviral transduction, cKIT positive cells were mixed in 1 to 10 or 1 to 1 ratio of PPM1D mutant to control cells and transplanted into irradiated syngeneic recipients. FIG. 4C is a plot showing that the percentage of PPM1D mutant cells increased >2.5 fold over two weeks in vivo while the percentage of control cells remained stable.

FIG. 5 provides an experimental schema of an in vivo competition experiment. Bone marrow chimaeras were generated by transplanting Mx-Cre Cas9 cKit⁺ Cas9 cells transduced with a BFP-tagged sgRNA targeting exon 6 of PPM1D or a tRFP-tagged control sgRNA into lethally-irradiated syngeneic recipients in a 1:5 ratio.

FIGS. 6A-6H show that PPM1D-mutant peripheral blood and bone marrow cells undergo expansion after cytarabine exposure in vivo. FIG. 6A is a plot showing flow cytometric analysis of peripheral blood lymphocytes in mice exposed to several rounds of cytarabine or vehicle treatment. PPM1D and control sgRNAs were identified through their fluorophores. FIG. 6B is a plot showing flow cytometric analysis of monocytes in mice exposed to several rounds of cytarabine or vehicle treatment. PPM1D and control sgRNAs were identified through their fluorophores. FIG. 6C is a plot showing flow cytometric analysis of granulocytes in mice exposed to several rounds of cytarabine or vehicle treatment. PPM1D and control sgRNAs were identified through their fluorophores. FIG. 6D is a plot showing change in the ratio of PPM1D sgRNAs to total sgRNAs (PPM1D plus control sgRNAs) after three rounds of treatment with cytarabine compared to pre-treatment, assessed by flow cytometric analysis of the sgRNA fluorophores in peripheral blood leukocytes. FIG. 6E is a plot showing change in the ratio of PPM1D sgRNAs to total sgRNAs (PPM1D plus control sgRNAs) after three rounds of treatment with cytarabine compared to pre-treatment, assessed by flow cytometric analysis of the sgRNA fluorophores in lymphocytes. FIG. 6F is a plot showing change in the ratio of PPM1D sgRNAs to total sgRNAs (PPM1D plus control sgRNAs) after three rounds of treatment with cytarabine compared to pre-treatment, assessed by flow cytometric analysis of the sgRNA fluorophores in monocytes. FIG. 6G is a plot showing change in the ratio of PPM1D sgRNAs to total sgRNAs (PPM1D plus control sgRNAs) after three rounds of treatment with cytarabine compared to pre-treatment, assessed by flow cytometric analysis of the sgRNA fluorophores in granulocytes. FIG. 6H is a plot of the ratio of PPM1D indels to total indels (control plus PPM1D) as identified through Next Generation Sequencing in cKit⁺ cells pre-transplant and post three rounds of cytarabine or vehicle treatment.

FIGS. 7A-7C shows a time course of Log-fold enrichment of sgRNAs targeting PPM1D. |FIG. 7A is a plot depicting Log-fold enrichment of sgRNAs targeting PPM1D (black dots) as assessed through Next Generation Sequencing of integrated sgRNAs in Molm13 cells exposed to cytarabine treatment versus vehicle treatment at 12 days. FIG. 7B is a plot depicting Log-fold enrichment of sgRNAs targeting PPM1D (black dots) as assessed through Next Generation Sequencing of integrated sgRNAs in Molm13 cells exposed to cytarabine treatment versus vehicle treatment at 20 days. FIG. 7C is a plot depicting Log-fold enrichment of sgRNAs targeting PPM1D (black dots) as assessed through Next Generation Sequencing of integrated sgRNAs in Molm13 cells exposed to cytarabine treatment versus vehicle treatment at 24 days. The line represents the locally weighted scatterplot smoothing (LOESS).

FIGS. 8A-8F show that truncating PPM1D mutations led to decreased degradation of PPM1D. FIG. 8A is a plot showing Log-fold enrichment of sgRNAs (black dots) in Molm13 cells exposed to cytarabine treatment versus vehicle treatment, 12 day time-point. The line represents the locally weighted scatterplot smoothing (LOESS) of 0.1. Overlaid are frame-shift and non-sense mutations (black bars) identified in the blood cells of 29,562 persons as described in FIG. 2A. FIG. 8B is a vector map of the degradation reporter vector, with different PPM1D cDNA constructs inserted. FIG. 8C is a graph showing EGFP/mCherry ratio for Molm13 cells with overexpression of wild type PPM1D, truncated PPM1D or the C-terminal end of PPM1D. FIG. 8D is a graph showing EGFP/mCherry ratio for Molm13 p53^(−/−) cells with overexpression of wild type PPM1D, truncated PPM1D or the C-terminal end of PPM1D. FIG. 8E is a graph showing EGFP/mCherry ratio in Molm13 cells before and after exposure to MG132 (10 μM, 6 hours), normalized to pre-treatment values. FIG. 8F is a plot showing cell viability analysis in Molm13 control cells (control), Molm13 PPM1D truncating mutant cells (PPM1D mutant) and Molm13 cells with overexpression of wild-type PPM1D (WT overexpression). Cells were exposed to increasing concentrations of cytarabine for 72 hours. For all experiments the following apply: *=p<0.05, **=p<0.01, ***=p<0.001, ****=p<0.0001.

FIGS. 9A-9G show that truncating PPM1D mutations abrogated the DNA damage response. FIG. 9A provides immunoblots showing that PPM1D mutant cells had decreased phosphorylation of p53 and Chk1 in response to treatment with Cytarabine. Whole cell lysates of Molm13 PPM1D-mutant and Molm13 control single cell clones exposed to 400 nM cytarabine for 4 hours were probed with anti-p53 Ser15 and anti-Chk1 Ser345. FIG. 9B is a graph showing percent Annexin V positive cells in cells treated with Cytarabine or vehicle. Molm13 PPM1D-mutant and control single cell clones exposed to 400 nM cytarabine or vehicle treatment for 24 hours were analyzed by Annexin V staining and flow cytometric analysis. FIG. 9C is a graph depicting percent viable cells from Molm13 PPM1D-mutant and control single cell clones after 24 hours of exposure to 100 nM cytarabine, as analyzed by BrdU staining and flow cytometric analysis. FIG. 9D is a heatmap of phosphosites that belong to the KEGG_P53 pathway and were significantly regulated with an FDR<0.1 in either Molm13 PPM1D mutant/wild-type at baseline (Mut/wt) or after 4 hour treatment with 400 nM cytarabine (AraC). FIG. 9E is a chart depicting the consensus sequence of PPM1D based on substrate analysis of 43 substrate candidates of PPM1D. FIG. 9F depicts 43 potential PPM1D substrate sites on pSer/Thr residues on 25 proteins. Phosphosites were significantly down-regulated in either Mut/wt of AraC treated or untreated samples (FDR<0.05) and upregulated for PPM1Di/ctrl (FDR<0.05). Only localized sites were considered. Figure discloses SEQ ID NOS 4-20 and 20-31, respectively, in order of appearance. FIG. 9G depicts a schema illustrating the components of the DNA-damage response pathway that are targeted by PPM1D in leukemia cells, based on the results from the phosphoproteomics analysis. Phospho-targets of PPM1D identified by mass spectrometry (FDR<0.1) are shown in bold. Predicted PPM1D target sites that were based on the identified consensus sequence with a glutamine at +1 and ≥2 acidic residues (p=3.595e-13, Fisher's exact test) are shown in italics.

FIGS. 10A-10F show that PPM1D inhibition with GSK2830371 reversed the aberrant PPM1D mutant phosphorylation pattern, reverses chemotherapy resistance, and selectively targets PPM1D-mutant cells. FIG. 10A provides immunoblots showing that PPM1D inhibition increased the phosphorylation of p53 during Cytarabine treatment. Whole cell lysate of Molm13 PPM1D-mutant singe cell clones 1 hour pretreated with the indicated concentrations of GSK2830371 and exposed to 400 nM cytarabine or vehicle were probed for p53 Ser15 and Actin as a loading control. FIG. 10B is a heatmap of phosphosites belonging to the KEGG_P53 pathway that are significantly regulated (FDR<0.1). Molm13 PPM1D mutant/wild-type after 4 hour treatment with 400 nM cytarabine (AraC) (Mut/wt) or Molm13 PPM1D-mutant cells treated with 400 nM AraC+1 μM PPM1D inhibitor GSK2830371/Molm13 PPM1D mut cells treated with 400 nM AraC (Mut AraC+iPPM1D/Mut AraC) for 4 hours. FIG. 10C is a plot showing that the sensitivity of PPM1D mutant cells to Cytarabine increased when combined with PPM1D inhibition. Viability analysis of Molm13 PPM1D-mutant cells pre-treated for 1 hour with 3 μM GSK2830371 or vehicle, and Molm13 control single cell clones, exposed to increasing doses of 72-hour cytarabine treatment. FIG. 10D is a plot showing that PPM1D inhibition reversed the competitive advantage of PPM1D mutant cells during treatment with Cytarabine. Competition experiment with Molm13 PPM1D-mutant pooled cells and control pooled cells mixed in resp. a 1:9 ratio and exposed to 100 nM cytarabine, 100 nM cytarabine plus 100 nM GSK2830371 or vehicle treatment. FIG. 10E is a plot showing that PPM1D mutant cells had an increased sensitivity to PPM1D inhibition with compound GSK2830371. 72 hour cell viability analysis in Molm13 PPM1D-mutant and control single cell clones after exposure to increasing doses of GSK2830371. FIG. 10F is a graph showing percent Annexin V positive cells in cells treated with PPM1D inhibitor or vehicle. Annexin V staining and flow cytometric analysis of Molm13 PPM1D-mutant and control single cell clones exposed to 3 μM of GSK2830371. *=p<0.05, **=p<0.01, ***=p<0.001

FIGS. 11A and 11B show that PPM1D inhibition reversed chemotherapy resistance. FIG. 11A is a plot showing that PPM1D mutant cells had an increased sensitivity to PPM1D inhibition with compound GSK2830371. FIG. 11B is a plot showing PPM1D mutant cells were sensitive to PPM1D inhibition with compound CCT007093. PPM1D mutant cells had an increased sensitivity to treatment with the PPM1D inhibitor CCT007093 in comparison to wild-type (wt) control cells.

FIG. 12 is a table of showing generation of PPM1D sgRNA sequences for the saturation mutagenesis CRISPR screen. Figure discloses sgRNA Target Sequences as SEQ ID NOs: 36-300, respectively, in order of appearance. Figure discloses Target Context Sequences as SEQ ID NOs: 301-565, respectively, in order of appearance.

DETAILED DESCRIPTION OF THE INVENTION

The invention features compositions and methods that are useful for treating a cancer in a subject, particularly a subject that is resistant to chemotherapy and/or has mutations in PPM1D. The invention also features compositions and methods that are useful for treating clonal hematopoiesis of indeterminate potential (CHIP) in a subject, particularly a subject that has mutations in PPM1D. The invention is based, at least in part, on the discovery that PPM1D truncating mutations caused clonal dominance and chemotherapy resistance, which could be reversed by PPM1D inhibition.

Results described herein demonstrate that truncating PPM1D mutations, which can be found in the blood of individuals with hematologic cancers, as well as in individuals with a pre-malignant state for hematologic cancers, and are causally associated with resistance to chemotherapy in both normal and malignant hematopoietic cells. Importantly, this finding allows for the reversal of clonal dominance and chemotherapy resistance caused by these mutations through the use of PPM1D inhibitors.

PPM1D mutations have been identified in the blood of individuals, particularly after exposure to chemotherapy. It was not known whether PPM1D mutations were causally related to blood cell chemotherapy resistance. Results described herein demonstrate a causal association, and also demonstrates that a therapy targeting PPM1D specifically can be used to treat malignant and non-malignant cells bearing PPM1D mutations with PPM1D inhibitor to reverse the chemotherapy resistance and suppress the neoplastic clone.

Described herein is a finding that truncating, gain of function PPM1D mutations cause clonal dominance and chemotherapy resistance specifically in hematopoietic cells. While amplification of PPM1D has been described in some solid tumors, and PPM1D mutations have been described to occur in the blood of cancer patients, no direct evidence for blood cell clonal dominance due to chemotherapy resistance to be caused by these truncating PPM1D mutations has been provided.

PPM1D inhibitors have been described to be effective in solid tumor cell lines and in vivo models that have overexpression of PPM1D, but they have not before been used in cell lines or in vivo models with truncating PPM1D mutations, nor have they been tested in hematologic cells. In addition, no studies have provided evidence for reversal of chemotherapy resistance and clonal dominance caused by PPM1D mutations in blood cells using PPM1D inhibitors.

In some aspects, the invention features a method of treating a cancer in a pre-identified subject, where the subject is pre-identified as having a mutation in a PPM1D polynucleotide or polypeptide relative to a reference. In some embodiments, the cancer is a hematologic cancer. Identification of patients with hematologic cancers who have PPM1D mutations should be selected for treatment with a PPM1D inhibitor. The inclusion of patients for this treatment (or studies) will be based on the presence of truncating PPM1D mutations as identified by DNA sequencing of blood, bone marrow, or tumor sample.

Further, methods described herein can be used as an intervention to prevent the development of future secondary hematologic malignancies and/or therapy-related hematological malignancy in those currently being treated for cancer or those who have been treated for cancer (and have a PPM1D clone). A significant proportion of individuals being treated for cancer later develop a secondary hematologic malignancy. This invention discloses a method to identify a group at high-risk of developing a secondary hematologic malignancy (i.e., the presence of a pre-existing PPM1D mutation), and of treating that group with a PPM1D inhibitor in combination with chemotherapy for their cancer to lower the risk of secondary malignancy. By “in combination” is meant before, during, or after chemotherapy.

In other aspects, the invention provides a method of increasing sensitivity or reversing resistance of a cancer cell to a chemotherapeutic agent. The methods described herein are useful for reversal or prevention of chemotherapy resistance caused by PPM1D mutations in patients with clonal hematopoiesis of indeterminate potential (CHIP). CHIP is defined as the presence of an expanded clonal hematopoietic population due to a somatic mutation in a hematopoietic stem cell. CHIP progresses to a frank malignancy at a rate of approximately 1% per year. Methods provided by the invention identify individuals with CHIP due to PPM1D mutations that can benefit from a PPM1D targeted therapy to prevent future malignancy.

In still other aspects, the invention provides targeted treatment of malignancies that have PPM1D mutations. In some aspects, the targeted treatment is an agent that inhibits the expression or activity of a PPM1D polynucleotide or polypeptide. In some embodiments, the agent is a small molecule PPM1D inhibitor. The treatment can be administered to patients with solid tumors or hematological malignancies that carry truncating PPM1D mutations, such as gliomas, myelodysplastic syndrome, or acute myeloid leukemia. The PPM1D inhibitor treatment can be combined with chemotherapy treatment, or given (neo)adjuvantly. The addition of a PPM1D inhibitor to the treatment protocol of patients with PPM1D mutations specifically targets PPM1D mutant clones, which confer chemotherapy resistance. In some embodiments, the treatment is administered to a patient with solid tumors and hematological malignancies. In some other embodiments, the treatment is administered to a patient having a truncating PPM1D mutation. In some embodiments, the treatment is administered to a patient with a solid tumor, a hematological malignancy and/or clonal hematopoiesis of indeterminate potential (CHIP).

PPM1D Mutations and Clonal Dominance

PPM1D (WIP1) is a known oncogene that has been associated with a poor prognosis in patients with solid tumors (Yang, H. et al., Tumor Biol 36, 2179-2184 (2014); PENG, T.-S. et al., Exp Ther Medicine 8, 430-434 (2014); Lu, X. et al., Cancer Metastasis Rev. 27, 123-35 (2008)). While overexpression and amplification of PPM1D are relatively common, mutations in PPM1D have only recently been described. In a seminal study by Ruark et al, PPM1D mutations were found to be strongly associated with breast and ovarian cancer (Ruark, E. et al., Nature 493, 406-10 (2013)). The mutations all clustered in the last exon of PPM1D, leading to a truncation of the protein. Intriguingly, the mutations were found in the lymphocyte DNA, but not the tumor DNA of these patients. Since then, several others groups have reported the presence of truncating PPM1D mutations in the blood, but not tumor tissue of patients with breast, ovarian and lung cancer (Zajkowicz, A. et al., Br. J. Cancer 112, 1114-20 (2015); Akbari, M. R. et al., J. Natl. Cancer Inst. 106, djt323 (2014)).

In addition to being found in the blood of cancer patients, somatic truncating PPM1D mutations were recently identified in hematopoietic cells of aging adults (Genovese, G. et al., N. Engl. J. Med. 371, 2477-87 (2014)). Again, the mutations were found to cluster in the last exon of the gene, leading to truncation of the protein. While PPMID was among the most commonly mutated genes in clonal hematopoiesis, it has in contrast to other CHIP mutations, not been associated with hematological malignancies until recently (Lindsley et al., N. Engl. J. Med. 376, 536-547 (2017)). PPM1D truncating mutations have been detected in myelodysplastic syndrome (MDS) and these mutations are strongly enriched in therapy related MDS (Lindsley et al., N. Engl. J. Med. 376, 536-547 (2017)).

Truncating mutations of PPM1D have been shown to cause gain of function of PPM1D, which is a member of the PP2C family of Ser/Thr protein phosphatases (Kleiblova, P. et al., J. Cell Biol. 201, 511-21 (2013); Jaiswal, S. et al., N. Engl. J. Med. 371, 2488-98 (2014); Xie, M. et al., Nat. Med. 20, 1472-8 (2014)). As its original name indicates, Wild-type p53 Induced Phosphatase 1 (Wip1) is induced by p53 and is best known for its role as a negative regulator of the stress response. Targets of PPM1D include p53, Chk1/Chk2, ATM and ATR.

The presence of PPM1D mutations in clonal hematopoiesis implies a clonal dominance phenotype for PPM1D mutant cells. What is more, the finding of PPM1D mutations in the blood of cancer patients, who are likely to have experienced genotoxic stress due to chemotherapy treatment, combined with the function of PPM1D as a negative regulator of p53, indicates that PPM1D mutant cells can selectively expand during genotoxic stress.

The results presented here provide evidence for clonal dominance and chemotherapy resistance caused by truncating, gain of function PPM1D mutations. Without being bound by theory, it is believed that this leads to preferential expansion of PPM1D mutant cells during genotoxic stress. While gain of function driver mutations in cancer are rare, mutations in PPM1D were the most common new mutations identified in clonal hematopoiesis. In addition, truncating PPM1D mutations were recently shown to occur in 6% of patients with high-risk myelodysplastic syndromes (MDS) and to be enriched in therapy-related myelodysplastic syndromes (t-MDS), where they occur in 15% of cases (Lindsley et al., N. Engl. J. Med. 376, 536-547 (2017)). While no studies have reported on the presence of PPM1D mutations in acute myeloid leukemia (AML), it is believed that future studies will identify these mutations in a subset of patients with secondary or therapy related AML.

The finding that PPM1D mutations are gain of function is of great clinical relevance, as gain of function mutations are more amenable to pharmacological intervention. Indeed, our results demonstrate reversal of PPM1D induced clonal dominance through PPM1D inhibition. In addition, results herein demonstrate that chemotherapy resistance caused by PPM1D mutations can be overturned by the addition of low-dose or high dose PPM1D inhibitors to chemotherapy treatment. The fact that these results were obtained using two mechanistically different PPM1D inhibitors, diminishes the chances of the results being due to a specific compound.

While the use of PPM1D inhibitors on solid tumor cell lines with amplification of PPM1D has been reported in the past, no studies have employed PPM1D inhibitors for truncating, gain-of-function PPM1D mutations (Gilmartin, A. G. et al., Nat. Chem. Biol. 10, 181-7 (2014); Rayter S et al., Oncogene. 27, 1036-1044 (2008)). In addition, the use of PPM1D inhibition in hematological malignancies has not before been shown. Finally, reversal of chemotherapy resistance and clonal dominance by PPM1D inhibition is a new and clinically relevant finding.

Lastly, in view of the strong biological relationship between PPM1D and p53, pharmacological intervention of PPM1D may provide a route to modulation of p53. Considering the central role of p53 in many tumors, and the difficulties of targeting this oncogene, modulation of p53 through PPM1D may open the door to effective treatments for a multitude of malignancies.

Methods of Treatment

Results herein demonstrate reversal of chemotherapy resistance by PPM1D inhibition, which is a new and clinically relevant finding. Thus, the present invention provides methods of treating a cancer, particularly chemotherapy-resistant cancer or cancer associated with a PPM1D mutation, and/or disorders or symptoms thereof, which comprise administering a therapeutically effective amount of a pharmaceutical composition comprising an agent that inhibits the expression or activity of a PPM1D polynucleotide or polypeptide herein (e.g., a PPM1D inhibitor or an inhibitory polynucleotide that reduces PPM1D expression) to a subject (e.g., a mammal such as a human). Thus, one embodiment is a method of treating a subject suffering from or susceptible to a cancer, particularly chemotherapy-resistant cancer or cancer associated with a PPM1D mutation, or disorder or symptom thereof. The method includes the step of administering to the mammal a therapeutic amount of an amount of an agent herein sufficient to treat the disease or disorder or symptom thereof, under conditions such that the disease or disorder is treated.

The methods herein include administering to the subject (including a subject identified as in need of such treatment) an effective amount of an agent described herein, or a composition described herein to produce such effect. Identifying a subject in need of such treatment can be in the judgment of a subject or a health care professional and can be subjective (e.g. opinion) or objective (e.g. measurable by a test or diagnostic method).

As used herein, the terms “treat,” treating,” “treatment,” and the like refer to reducing or ameliorating a disorder and/or symptoms associated therewith. It will be appreciated that, although not precluded, treating a disorder or condition does not require that the disorder, condition or symptoms associated therewith be completely eliminated.

As used herein, the terms “prevent,” “preventing,” “prevention,” “prophylactic treatment” and the like refer to reducing the probability of developing a disorder or condition in a subject, who does not have, but is at risk of or susceptible to developing a disorder or condition.

The therapeutic methods of the invention (which include prophylactic treatment) in general comprise administration of a therapeutically effective amount of the agents herein, such as an agent that inhibits the expression or activity of a PPM1D polynucleotide or polypeptide herein, to a subject (e.g., animal, human) in need thereof, including a mammal, particularly a human. Such treatment will be suitably administered to subjects, particularly humans, suffering from, having, susceptible to, or at risk for a disease, disorder, or symptom thereof. Determination of those subjects “at risk” can be made by any objective or subjective determination by a diagnostic test or opinion of a subject or health care provider (e.g., genetic test, enzyme or protein marker, PPM1D mutation, family history, and the like). The agents herein may be also used in the treatment of any other disorders in which a PPM1D mutation may be implicated.

Pharmaceutical Compositions

The present invention features compositions useful for treating or preventing a cancer, chemotherapy-resistant cancer, a cancer associated with a PPM1D mutation, clonal hematopoiesis of indeterminate potential (CHIP), or clonal hematopoiesis associated with a PPM1D mutation in a subject. In some embodiments, the composition comprises one or more of a therapeutic agent as described herein (e.g., an agent that inhibits the expression or activity of a PPM1D polynucleotide or polypeptide, a chemotherapeutic agent, or any combination thereof). In some embodiments, the therapeutic agent is a small molecule PPM1D inhibitor. In some other embodiments, the therapeutic agent is an inhibitory polynucleotide that inhibits expression of PPM1D. In some embodiments, the therapeutic agent is a chemotherapeutic agent. In some embodiments, the composition further comprises a vehicle for intracellular delivery of a polypeptide or polynucleotide (e.g., a liposome).

The administration of a composition comprising a therapeutic agent herein for the treatment or prevention of a cancer, particularly chemotherapy resistant and/or PPM1D mutation associated cancer or treating clonal hematopoiesis of indeterminate potential (CHIP)), particularly associated with a PPM1D mutation, may be by any suitable means that results in a concentration of the therapeutic that, combined with other components, is effective in ameliorating, reducing, or stabilizing a cancer or clonal hematopoiesis of indeterminate potential in a subject. In some embodiments, the cancer is a blood cancer, such as acute myeloid leukemia. The composition may be administered systemically, for example, formulated in a pharmaceutically-acceptable buffer such as physiological saline. Preferable routes of administration include, for example, subcutaneous, intravenous, interperitoneally, intramuscular, or intradermal injections that provide continuous, sustained levels of the agent in the patient. The amount of the therapeutic agent to be administered varies depending upon the manner of administration, the age and body weight of the patient, and with the clinical symptoms of the cancer. Generally, amounts will be in the range of those used for other agents used in the treatment of cancers, although in certain instances lower amounts will be needed because of the increased specificity of the agent. A composition is administered at a dosage that decreases effects or symptoms of cancer as determined by a method known to one of ordinary skill in the art.

The therapeutic agent (e.g., an agent that inhibits the expression or activity of a PPM1D polynucleotide or polypeptide, a chemotherapeutic agent, or any combination thereof) may be contained in any appropriate amount in any suitable carrier substance, and is generally present in an amount of 1-95% by weight of the total weight of the composition. The composition may be provided in a dosage form that is suitable for parenteral (e.g., subcutaneously, intravenously, intramuscularly, or intraperitoneally) administration route. The pharmaceutical compositions may be formulated according to conventional pharmaceutical practice (see, e.g., Remington: The Science and Practice of Pharmacy (20th ed.), ed. A. R. Gennaro, Lippincott Williams & Wilkins, 2000 and Encyclopedia of Pharmaceutical Technology, eds. J. Swarbrick and J. C. Boylan, 1988-1999, Marcel Dekker, New York).

Pharmaceutical compositions according to the invention may be formulated to release the active agent substantially immediately upon administration or at any predetermined time or time period after administration. The latter types of compositions are generally known as controlled release formulations, which include (i) formulations that create a substantially constant concentration of the drug within the body over an extended period of time; (ii) formulations that after a predetermined lag time create a substantially constant concentration of the drug within the body over an extended period of time; (iii) formulations that sustain action during a predetermined time period by maintaining a relatively, constant, effective level in the body with concomitant minimization of undesirable side effects associated with fluctuations in the plasma level of the active substance (sawtooth kinetic pattern); (iv) formulations that localize action by, e.g., spatial placement of a controlled release composition adjacent to or in contact with an organ, such as the liver; (v) formulations that allow for convenient dosing, such that doses are administered, for example, once every one or two weeks; and (vi) formulations that target a cancer using carriers or chemical derivatives to deliver the therapeutic agent to a particular cell type (e.g., liver cell). For some applications, controlled release formulations obviate the need for frequent dosing during the day to sustain the plasma level at a therapeutic level.

Any of a number of strategies can be pursued in order to obtain controlled release in which the rate of release outweighs the rate of metabolism of the agent in question. In one example, controlled release is obtained by appropriate selection of various formulation parameters and ingredients, including, e.g., various types of controlled release compositions and coatings. Thus, the therapeutic is formulated with appropriate excipients into a pharmaceutical composition that, upon administration, releases the therapeutic in a controlled manner. Examples include single or multiple unit tablet or capsule compositions, oil solutions, suspensions, emulsions, microcapsules, microspheres, molecular complexes, nanoparticles, patches, and liposomes.

The pharmaceutical composition may be administered parenterally by injection, infusion or implantation (subcutaneous, intravenous, intramuscular, intraperitoneal, or the like) in dosage forms, formulations, or via suitable delivery devices or implants containing conventional, non-toxic pharmaceutically acceptable carriers and adjuvants. The formulation and preparation of such compositions are well known to those of ordinary skill in the art of pharmaceutical formulation. Formulations can be found in Remington: The Science and Practice of Pharmacy, supra.

Compositions for parenteral use may be provided in unit dosage forms (e.g., in single-dose ampoules), or in vials containing several doses and in which a suitable preservative may be added (see below). The composition may be in the form of a solution, a suspension, an emulsion, an infusion device, or a delivery device for implantation, or it may be presented as a dry powder to be reconstituted with water or another suitable vehicle before use. Apart from the active agent that reduces or ameliorates a cancer, the composition may include suitable parenterally acceptable carriers and/or excipients. The active therapeutic agent(s) (e.g., an agent that inhibits the expression or activity of a PPM1D polynucleotide or polypeptide, a chemotherapeutic agent, or any combination thereof, as described herein) may be incorporated into microspheres, microcapsules, nanoparticles, liposomes, or the like for controlled release. Furthermore, the composition may include suspending, solubilizing, stabilizing, pH-adjusting agents, tonicity adjusting agents, and/or dispersing, agents.

In some embodiments, the composition comprising the active therapeutic (e.g., an agent that inhibits the expression or activity of a PPM1D polynucleotide or polypeptide, a chemotherapeutic agent, or any combination thereof), is formulated for intravenous delivery. As indicated above, the pharmaceutical compositions according to the invention may be in the form suitable for sterile injection. To prepare such a composition, the suitable therapeutic(s) are dissolved or suspended in a parenterally acceptable liquid vehicle. Among acceptable vehicles and solvents that may be employed are water, water adjusted to a suitable pH by addition of an appropriate amount of hydrochloric acid, sodium hydroxide or a suitable buffer, 1,3-butanediol, Ringer's solution, and isotonic sodium chloride solution and dextrose solution. The aqueous formulation may also contain one or more preservatives (e.g., methyl, ethyl or n-propyl p-hydroxybenzoate). In cases where one of the agents is only sparingly or slightly soluble in water, a dissolution enhancing or solubilizing agent can be added, or the solvent may include 10-60% w/w of propylene glycol or the like.

Polynucleotide Therapy

Another therapeutic approach for treating or preventing a cancer, particularly a chemotherapy resistant and/or PPM1D mutation associated cancer, or clonal hematopoiesis of indeterminate potential (CHIP), particularly associated with a PPM1D mutation, is polynucleotide therapy using an inhibitory polynucleotide that reduces PPM1D expression. In some aspects, the invention provides a therapeutic composition comprising an inhibitory polynucleotide that reduces PPM1D expression (e.g., siRNA).

Provided herein are inhibitory polynucleotides that reduce PPM1D expression. Delivery or expression of such polynucleotides in a cell, such as a cell in a subject having a chemotherapy resistant cancer associated with PPM1D mutation, is expected to increase sensitivity to chemotherapy in the subject. Such inhibitory polynucleotides can be delivered to cells of a subject having a cancer (in particular, subjects having a chemotherapy resistant and/or PPM1D mutation associated cancer) or clonal hematopoiesis of indeterminate potential (in particular, CHIP associated with a PPM1D mutation). The inhibitory polynucleotides must be delivered to or expressed in the cells of a subject such that expression levels of PPM1D in the cells are effectively reduced.

Transducing viral (e.g., retroviral, adenoviral, and adeno-associated viral) vectors can be used for somatic cell gene therapy, especially because of their high efficiency of infection and stable integration and expression (see, e.g., Cayouette et al., Human Gene Therapy 8:423-430, 1997; Kido et al., Current Eye Research 15:833-844, 1996; Bloomer et al., Journal of Virology 71:6641-6649, 1997; Naldini et al., Science 272:263-267, 1996; and Miyoshi et al., Proc. Natl. Acad. Sci. U.S.A. 94:10319, 1997). For example, a polynucleotide encoding an inhibitory polynucleotide that reduces PPM1D expression, can be cloned into a retroviral vector and expression can be driven from its endogenous promoter, from the retroviral long terminal repeat, or from a promoter specific for a target cell type of interest. Other viral vectors that can be used include, for example, a vaccinia virus, a bovine papilloma virus, or a herpes virus, such as Epstein-Barr Virus (also see, for example, the vectors of Miller, Human Gene Therapy 15-14, 1990; Friedman, Science 244:1275-1281, 1989; Eglitis et al., BioTechniques 6:608-614, 1988; Tolstoshev et al., Current Opinion in Biotechnology 1:55-61, 1990; Sharp, The Lancet 337:1277-1278, 1991; Cornetta et al., Nucleic Acid Research and Molecular Biology 36:311-322, 1987; Anderson, Science 226:401-409, 1984; Moen, Blood Cells 17:407-416, 1991; Miller et al., Biotechnology 7:980-990, 1989; Le Gal La Salle et al., Science 259:988-990, 1993; and Johnson, Chest 107:77S-83S, 1995). Retroviral vectors are particularly well developed and have been used in clinical settings (Rosenberg et al., N. Engl. J. Med 323:370, 1990; Anderson et al., U.S. Pat. No. 5,399,346). In some embodiments, a viral vector is used to administer an inhibitory polynucleotide that reduces PPM1D expression systemically.

Non-viral approaches can also be employed for the introduction of the therapeutic to a cell of a patient requiring treatment of a cancer (particularly, a chemotherapy resistant and/or PPM1D mutation associated cancer). For example, a nucleic acid molecule can be introduced into a cell by administering the nucleic acid in the presence of lipofection (Feigner et al., Proc. Natl. Acad. Sci. U.S.A. 84:7413, 1987; Ono et al., Neuroscience Letters 17:259, 1990; Brigham et al., Am. J. Med. Sci. 298:278, 1989; Staubinger et al., Methods in Enzymology 101:512, 1983), asialoorosomucoid-polylysine conjugation (Wu et al., Journal of Biological Chemistry 263:14621, 1988; Wu et al., Journal of Biological Chemistry 264:16985, 1989), or by micro-injection under surgical conditions (Wolff et al., Science 247:1465, 1990). In some embodiments, the nucleic acids are administered in combination with a liposome and protamine.

Gene transfer can also be achieved using non-viral means involving transfection in vitro. Such methods include the use of calcium phosphate, DEAE dextran, electroporation, and protoplast fusion. Liposomes can also be potentially beneficial for delivery of DNA into a cell. Transplantation of a polynucleotide (e.g., DNA) encoding inhibitory polynucleotides (e.g., siRNA) into the affected tissues of a patient can also be accomplished by transferring a polynucleotide encoding the inhibitory polynucleotide into a cultivatable cell type ex vivo (e.g., an autologous or heterologous primary cell or progeny thereof), after which the cell (or its descendants) are injected into a targeted tissue.

cDNA expression for use in polynucleotide therapy methods can be directed from any suitable promoter (e.g., the human cytomegalovirus (CMV), simian virus 40 (SV40), or metallothionein promoters), and regulated by any appropriate mammalian regulatory element. For example, if desired, enhancers known to preferentially direct gene expression in specific cell types can be used to direct the expression of a nucleic acid. The enhancers used can include, without limitation, those that are characterized as tissue- or cell-specific enhancers. Alternatively, if a genomic clone is used as a therapeutic construct, regulation can be mediated by the cognate regulatory sequences or, if desired, by regulatory sequences derived from a heterologous source, including any of the promoters or regulatory elements described above.

Delivery of polynucleotides of the invention may also include or be performed in combination with gene or genome editing methods, such as CRISPR-Cas systems, to introduce polynucleotides encoding inhibitory polynucleotide PPM1D in cells. Gene or genome editing methods such as CRISPR-Cas systems are further described in for example, Sander et al. (2014), Nature Biotechnology 32, 347-355; Hsu et al. (2014), Cell 157(6): 1262-1278.

Stratifying Patient Population and Monitoring Effectiveness of Chemotherapy

The results of studies described herein provide evidence for chemotherapy resistance caused by truncating, gain of function PPM1D mutations. Thus, information on PPM1D status in a subject having cancer may predict clinical response of the cancer to chemotherapeutic agents, particularly DNA damaging agents. Accordingly, in one aspect, the invention provides a method of identifying a subject having a cancer that is resistant or sensitive to a chemotherapeutic agent, particularly a DNA damaging agent. The method includes the step of measuring a level and/or sequence of a PPM1D polynucleotide or polypeptide in a biological sample obtained from the subject. In some embodiments, a subject is identified as having a cancer that is resistant to a chemotherapeutic agent if a mutation in a PPM1D polynucleotide or polypeptide relative to a reference sequence is detected. In some embodiments, a subject is identified as having a cancer that is sensitive to a chemotherapeutic agent if a mutation in a PPM1D polynucleotide or polypeptide relative to a reference sequence is not detected. In some embodiments, the chemotherapeutic agent is a DNA damaging agent. In some embodiments, the chemotherapeutic agent is Cytarabine, Doxorubicin, Cyclophosphamide, or Cisplatin.

Diagnostic analysis of PPM1D status should be performed in cancer patients who are receiving, have received, or are expected to receive chemotherapy, particularly cancer patients who are receiving chemotherapy and have developed resistance to chemotherapy. A subject identified as sensitive to chemotherapeutic agent can be administered a chemotherapeutic agent. Over time, many patients treated with a chemotherapeutic agent acquire resistance to the therapeutic effects of the chemotherapeutic agent. The early identification of resistance to chemotherapy in a cancer patient can be important to patient survival because it allows for the selection of alternative therapies. Subjects identified as having a cancer resistant to a chemotherapeutic agent are identified as in need of alternative treatment. In some embodiments, a subject identified as in need of alternative treatment is administered an alternative therapy to chemotherapy or is recommended to receive an alternative therapy. In certain embodiments, the alternative therapy includes an agent that inhibits expression or activity of PPM1D polypeptide or polynucleotide. In some embodiments, the alternative therapy is a combination of an agent that inhibits expression or activity of PPM1D polypeptide or polynucleotide and a chemotherapeutic agent. In particular embodiments, the agent that inhibits expression or activity of PPM1D polypeptide or polynucleotide is a PPM1D inhibitor. In some embodiments, the PPM1D inhibitor is GSK2830371, CCT007093, or an analog thereof.

Methods of monitoring the sensitivity or resistance to a chemotherapeutic agent are useful in managing subject treatment. The results presented here provide evidence for clonal dominance and chemotherapy resistance caused by truncating, gain of function PPM1D mutations. Without being bound by theory, it is believed that this leads to preferential expansion of PPM1D mutant cells during genotoxic stress. Accordingly, monitoring the fraction of a cell population that harbors PPM1D mutations can be used to monitor a patient's resistance or sensitivity to chemotherapy.

Thus, in some embodiments, alterations in a polynucleotide or polypeptide of PPM1D (e.g., sequence, level, biological activity) are analyzed before and again after subject management or treatment. In these cases, the methods are used to monitor the status of sensitivity to a chemotherapeutic agent. The level, biological activity, or sequence of a polypeptide or polynucleotide of PPM1D may be assayed before treatment, during treatment, or following the conclusion of a treatment regimen. In some embodiments, multiple assays (e.g., 2, 3, 4, 5) are made at one or more of those times to assay resistance to a chemotherapeutic agent.

In one embodiment, the method includes the step of determining a level and/or sequence of a diagnostic marker (e.g., PPM1D polynucleotide or polypeptide) or diagnostic measurement (e.g., screen, assay) in a subject suffering from or susceptible to cancer or a disorder or symptoms thereof, in which the subject has been administered a therapeutic amount of an agent herein (e.g., a PPM1D inhibitor and/or a chemotherapeutic agent) sufficient to treat the disease or symptoms thereof. The level of PPM1D polypeptide or polynucleotide determined in the method can be compared to known levels or sequence of PPM1D polypeptide or polynucleotide in either healthy normal controls or in other afflicted patients to establish the subject's disease status. In some embodiments, the level of PPM1D polynucleotide or polypeptide containing a mutation (“mutant PPM1D”) in a biological sample obtained from the subject relative to a reference is determined. The reference can be the level of wild-type PPM1D polynucleotide or polypeptide in the biological sample. In some embodiments, a second level of mutant PPM1D polypeptide or polynucleotide in the subject is determined at a time point later than the determination of the first level, and the two levels are compared to monitor the course of disease or the efficacy of the therapy. In certain embodiments, a pre-treatment level of mutant PPM1D polypeptide or polynucleotide in the subject is determined prior to beginning treatment according to this invention; this pre-treatment level of mutant PPM1D polypeptide or polynucleotide can then be compared to the level of mutant PPM1D polypeptide or polynucleotide in the subject after the treatment commences, to determine the efficacy of the treatment.

Alterations in polynucleotides or polypeptides of PPM1D (e.g., sequence, level, biological activity) are detected in a biological sample obtained from a patient that has or has a propensity to develop a cancer. Biological samples include tissue samples (e.g., cell samples, biopsy samples). Biological samples that are used to evaluate the herein disclosed markers include without limitation tumor cells, blood, serum, plasma, urine. In one embodiment, the biological sample is blood.

While the examples provided herein describe specific methods of detecting levels of polynucleotides or polypeptides of PPM1D, those of ordinary skill in the art appreciate that the invention is not limited to such methods. The biomarkers of this invention can be detected or quantified by any suitable method. For example, methods include, but are not limited to real-time PCR, Southern blot, PCR, mass spectroscopy, and/or antibody binding. Methods for detecting a mutation of the invention include immunoassay, direct sequencing, and probe hybridization to a polynucleotide encoding the mutant polypeptide.

Combination Therapies

Also provided herein are methods of increasing sensitivity to a chemotherapeutic agent, particularly a DNA damage agent, in a subject having a cancer (in particular, a chemotherapy resistant and/or PPM1D mutation associated cancer). The findings herein indicate that a combination of a chemotherapeutic agent and an agent that inhibits expression or activity of PPM1D polypeptide or polynucleotide would benefit patients with PPM1D mutations (particularly, a PPM1D truncation mutation that is a gain-of-function mutation).

Thus, in some embodiments, a therapeutic composition comprising a chemotherapeutic agent may be administered to a subject having a cancer, in combination with a composition comprising an agent that inhibits expression or activity of PPM1D polypeptide or polynucleotide. In particular embodiments, the subject is identified as resistant to a chemotherapeutic agent. In certain embodiments, the subject is identified as having a PPM1D mutation. An agent that inhibits expression or activity of PPM1D polypeptide or polynucleotide (e.g., an inhibitory polynucleotide that reduces PPM1D expression or a small molecule PPM1D inhibitor) is administered to a subject identified as resistant to a chemotherapeutic agent. In some embodiments, the chemotherapeutic agent is a DNA damaging agent. In some embodiments, the chemotherapeutic agent is Cytarabine, Doxorubicin, Cyclophosphamide, or Cisplatin. In some embodiments, the small molecule PPM1D inhibitor is GSK2830371, CCT007093, or an analog thereof.

Kits

The invention provides kits for treating or preventing a cancer or clonal hematopoiesis of indeterminate potential (CHIP) in a subject and/or identifying resistance or sensitivity to a chemotherapeutic agent in a subject having a cancer. A kit of the invention provides a capture reagent (e.g., a primer or hybridization probe specifically binding to a PPM1D polynucleotide) for measuring relative expression level or a sequence of a marker (e.g., PPM1D).

In one embodiment, the kit includes a diagnostic composition comprising a capture reagent detecting a PPM1D polynucleotide or polypeptide. In one embodiment, the capture reagent detecting a polynucleotide of PPM1D is a primer or hybridization probe that specifically binds to a PPM1D polynucleotide.

The kits may further comprise a therapeutic composition comprising a chemotherapeutic agent. In some embodiments, the chemotherapeutic agent is a DNA damaging agent. In some embodiments, the chemotherapeutic agent is Cytarabine, Doxorubicin, Cyclophosphamide, or Cisplatin.

The kits may also further comprise a therapeutic composition comprising an agent that inhibits expression or activity of a PPM1D polypeptide or polynucleotide. In some embodiments, the agent that inhibits expression or activity of a PPM1D polypeptide or polynucleotide is an inhibitory polynucleotide that reduces PPM1D expression. In particular embodiments, the agent that inhibits expression or activity of a PPM1D polypeptide or polynucleotide is a small molecule PPM1D inhibitor. In some embodiments, the PPM1D inhibitor is GSK2830371, CCT007093, or an analog thereof.

In some embodiments, the kit comprises a sterile container which contains a therapeutic composition; such containers can be boxes, ampoules, bottles, vials, tubes, bags, pouches, blister-packs, or other suitable container forms known in the art. Such containers can be made of plastic, glass, laminated paper, metal foil, or other materials suitable for holding medicaments.

If desired, the kit further comprises instructions for administering the therapeutic combinations of the invention. In particular embodiments, the instructions include at least one of the following: description of the therapeutic agent; dosage schedule and administration for enhancing anti-tumor activity; precautions; warnings; indications; counter-indications; over dosage information; adverse reactions; animal pharmacology; clinical studies; and/or references. The instructions may be printed directly on the container (when present), or as a label applied to the container, or as a separate sheet, pamphlet, card, or folder supplied in or with the container.

The practice of the present invention employs, unless otherwise indicated, conventional techniques of molecular biology (including recombinant techniques), microbiology, cell biology, biochemistry and immunology, which are well within the purview of those of ordinary skill in the art. Such techniques are explained fully in the literature, such as, “Molecular Cloning: A Laboratory Manual”, second edition (Sambrook, 1989); “Oligonucleotide Synthesis” (Gait, 1984); “Animal Cell Culture” (Freshney, 1987); “Methods in Enzymology” “Handbook of Experimental Immunology” (Weir, 1996); “Gene Transfer Vectors for Mammalian Cells” (Miller and Calos, 1987); “Current Protocols in Molecular Biology” (Ausubel, 1987); “PCR: The Polymerase Chain Reaction”, (Mullis, 1994); “Current Protocols in Immunology” (Coligan, 1991). These techniques are applicable to the production of the polynucleotides and polypeptides of the invention, and, as such, may be considered in making and practicing the invention. Particularly useful techniques for particular embodiments will be discussed in the sections that follow.

The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to make and use the assay, screening, and therapeutic methods of the invention, and are not intended to limit the scope of what the inventors regard as their invention.

EXAMPLES Example 1: Truncating Mutations of PPM1D Lead to Chemotherapy Resistance

To study the role of PPM1D mutations in chemotherapy resistance, mutations in PPM1D were induced using the CRISPR-Cas9 system. The sgRNA is located in the last exon of the gene (FIG. 1A), similar to where truncating mutations in patients occur (Ruark, E. et al. Nature 493, 406-10 (2013); Zajkowicz, A. et al. Br. J. Cancer 112, 1114-20 (2015); Akbari, M. R. et al. J. Natl. Cancer Inst. 106, djt323 (2014); Genovese, G. et al. N. Engl. J. Med. 371, 2477-87 (2014); Xie, M. et al. Nat. Med. 20, 1472-8 (2014). Molm13 cells were transduced with a CRISPR-Cas9 lentivirus targeting hPPM1D, or a non-targeting guide. The presence of mutations was confirmed by Next Generation Sequencing. Frameshift mutations of PPM1D led to truncation and overexpression of the protein in subcloned and pooled Molm13 cells (FIG. 1B). Using sequence verified PPM1D mutant (fs) and empty vector control Molm13 cells, the effects of mutant and wild type PPM1D in the response to DNA damaging chemotherapy were analyzed. The therapies included Cytarabine, Doxorubicin, Cyclophosphamide and Cisplatin. Cell viability analysis in the presence of increasing drug concentrations demonstrated an increased resistance to Cytarabine in PPM1D mutant cells compared to empty vector controls. (FIG. 1C).

Whether PPM1D mutations conferred a competitive advantage during chemotherapy treatment was tested. In order to simulate a PPM1D mutant, subclonal environment similar to that seen in clonal hematopoiesis, a competition experiment in which pooled PPM1D mutant Molm13 cells were mixed with Molm13 control cells in a 1:99 ratio was performed. The mixed populations were treated with DNA damaging therapies, including Cytarabine and Cyclophosphamide, or DMSO every four days. Chemotherapy treatment induced a significant competitive advantage of PPM1D mutant cells, leading to an over 100-fold increase in the number of PPM1D mutant cells during treatment. Within 25 days of treatment, the mixed population was entirely taken over by PPM1D mutant cells (FIGS. 1D and 1E). As expected, exposure to DMSO did not select for PPM1D mutant cells.

The PPM1D gene has recently been found to be commonly somatically mutated in therapy-related myeloid neoplasms (t-MNs), clonal hematopoiesis of indeterminate potential (CHIP), and in the blood of patients with ovarian cancer, breast cancer and lung cancer (Jaiswal, S. et al. N. Engl. J. Med. 371, 2488-98 (2014); Genovese, G. et al. N. Engl. J. Med. 371, 2477-87 (2014); Xie, M. et al. Nat. Med. 20, 1472-8 (2014); Ruark, E. et al. Nature 493, 406-10 (2013); Zajkowicz, A. et al. Br. J. Cancer 112, 1114-20 (2015); Akbari, M. R. et al. J. Natl. Cancer Inst. 106, djt323 (2014); Pharoah, P. D. et al. J. Natl. Cancer Inst. 108, (2016); Swisher, E. M. et al. JAMA Oncol (2016); Gibson, C. J. et al. J. Clin. Oncol. JCO2016716712 (2017)). Mutations in PPM1D and TP53 are more highly associated with prior exposure to chemotherapy than any other mutations in myelodysplastic syndrome (MDS) (Lindsley, R. C. et al. N. Engl. J. Med. 376, 536-547 (2017)). PPM1D encodes a serine-threonine phosphatase that is transcriptionally upregulated in a p53-dependent manner in response to DNA damage (Gibson, C. J. et al. J. Clin. Oncol. JCO2016716712 (2017)). PPM1D in turn negatively regulates p53 and several members of the DNA damage response pathway (also termed “DDR”) (Lu, X. et al. Cell Cycle 4, 4060-4064 (2005); Fujimoto, H. et al. Cell Death Differ. 13, 1170-80 (2006); Takekawa, M. et al. EMBO J. 19, 6517-26 (2000)), and hence has been proposed to be a primary homeostatic regulator of the DNA damage response pathway, facilitating return to steady state after the cells have repaired damaged DNA (Lu, X. et al. Cell Cycle 4, 4060-4064 (2005); Lu, X. et al. Cancer Metastasis Rev. 27, 123-35 (2008)).

PPM1D gene in exome sequencing data from the peripheral blood of 29,562 individuals (Jaiswal, S. et al. N. Engl. J. Med. 371, 2488-98 (2014); Genovese, G. et al. N. Engl. J. Med. 371, 2477-87 (2014)) was analyzed to define the spectrum of genetic lesions and found localization of somatic frame-shift and nonsense mutations exclusively in exon 6, which would produce a protein truncated downstream of amino acid 400 (FIG. 2A). These PPM1D mutations match those observed in therapy-related myeloid neoplasms and in the blood of cancer patients who have received chemotherapy (Ruark, E. et al. Nature 493, 406-10 (2013); Zajkowicz, A. et al. Br. J. Cancer 112, 1114-20 (2015); Akbari, M. R. et al. J. Natl. Cancer Inst. 106, djt323 (2014); Swisher, E. M. et al. JAMA Oncol (2016)).

To study the sensitivity of PPM1D truncating mutations to chemotherapy exposure, frame-shift mutations were introduced in the PPM1D gene in Molm13 AML cells, which are TP53 wild-type, using CRISPR-Cas9. Exon 6 frame-shift mutations caused truncation and overexpression of PPM1D (FIG. 2B). PPM1D-mutant cells, compared to control cells expressing a non-targeting sgRNA, had increased viability at 72 hours in the presence of cytotoxic chemotherapeutic agents commonly used in the treatment of hematologic malignancies and solid tumors, such as cytarabine, cyclophosphamide, and cisplatin (FIGS. 2C-2E). To examine whether PPM1D-mutant cells have a competitive advantage relative to control cells over a longer time period, a competition experiment was performed. PPM1D-mutant Molm13 cells were mixed with control cells in a 1:25 ratio and exposed to chemotherapy or vehicle. Following exposure to chemotherapeutic agents, the PPM1D-mutant cells gained a competitive advantage, comprising more than 95% of cells within 24 days (FIGS. 2F-2H). When cells were cultured in the presence of vehicle instead of chemotherapy, PPM1D-mutant cells did not have a competitive advantage (FIGS. 2E-2G; 3A-3C). These findings demonstrate that PPM1D truncating mutations conferred chemotherapy resistance, leading to a competitive advantage of PPM1D-mutant leukemia cells under the selective pressure of chemotherapy.

Example 2: Truncation of PPM1D LED to Clonal Dominance

In view of the presence of PPM1D mutations in clonal hematopoiesis, it was hypothesized that PPM1D mutations confer clonal dominance. In order to study this in vitro, a serial replating assay was performed in which murine cKIT positive cells were transduced with a CRISPR-Cas9 targeting mPPM1D or a non-targeting CRISPR-Cas9 control guide. PPM1D mutant cKIT positive cells grew more colonies per replating, and could be replated more often than control cells (FIG. 4A).

To test directly whether PPM1D mutations lead to clonal dominance, mix bone marrow chimaeras containing both PPM1D mutant and control cells were generated (FIG. 4B). A >2.5 fold increase in the percentage of PPM1D mutant cells over a two-week period was observed, while the percentage of control cells remained stable (FIG. 4C).

Whether PPM1D mutations confer resistance to chemotherapy in vivo was examined. In another experiment, bone marrow chimeras were generated using Mx-Cre Cas9 c-Kit⁺ cells that were transduced with a BFP-tagged sgRNA targeting exon 6 of PPM1D or a tRFP-tagged control sgRNA and transplanted into lethally-irradiated syngeneic recipients in a 1:5 ratio (FIG. 5). Mice were treated with cytarabine or vehicle after hematopoietic reconstitution. A significant, selective increase of PPM1D-mutant cells in the peripheral blood was observed after cytarabine treatment (FIGS. 2F; 6A-6G). Without being bound by theory, this indicated that PPM1D-mutant cells had a competitive advantage over control cells in vivo after exposure to genotoxic stress. PPM1D-mutant hematopoietic stem and progenitor cells in the bone marrow were also increased at 12 weeks following 3 rounds of cytarabine (FIG. 6H).

Example 3: Chemotherapy Exposure Selects for Specific Mutations in PPM1D

Whether chemotherapy exposure selects for specific mutations in PPM1D was investigated. A saturation mutagenesis CRISPR screen was performed in which cells were infected with a CRISPR library of 265 sgRNAs tiling all exons of PPM1D (FIG. 12), at a multiplicity of infection of 1000 so that cells would receive zero or one sgRNA per cell. Cells were treated for 24 days with cytarabine or vehicle, and the representation of sgRNAs in the two groups was determined by sequencing the integrated sgRNAs. A selective enrichment of sgRNAs targeting amino acids 400-585 (exon 6) of PPM1D was observed in cells treated with chemotherapy compared to vehicle. Without being bound by theory, this indicated that these sgRNAs introduce PPM1D mutations that confer resistance to chemotherapy (FIGS. 7A-7C, FIG. 12). This region tightly overlaps with the region of PPM1D mutations identified in individuals with clonal hematopoiesis of indeterminate potential (CHIP) (FIG. 8A). In contrast, sgRNAs targeting the last 20 amino acids of exon 6 did not have a selective advantage during chemotherapy treatment and no human CHIP or t-MN mutations have been identified to occur in this region. These studies demonstrated that the non-random localization of somatic PPM1D mutations in patients with therapy-related malignancies corresponded to the CRISPR-generated mutations that cause chemotherapy resistance.

Because PPM1D exon 6 mutations led to increased protein expression, and previous studies have indicated that PPM1D may be targeted to the proteasome (Kleiblova, P. et al. J. Cell Biol. 201, 511-21 (2013)), it was hypothesized that the C-terminal domain of PPM1D contains a sequence that mediates degradation of PPM1D. A reporter vector was generated in which wild-type PPM1D cDNA (wt), PPM1D truncation mutants, or the last 80 amino-acids (C-terminal region) were cloned in frame with GFP, so the level of expression of the PPM1D sequences could be monitored by GFP expression (FIG. 8B, Table 1).

TABLE 1 Reporter Vector Sequences Con- struct Sequence WT ATGGCGGGGCTGTACTCGCTGGGAGTGAGCGTCTTCTCCG (SEQ ACCAGGGCGGGAGGAAGTACATGGAGGACGTTACTCAAAT ID NO: CGTTGTGGAGCCCGAACCGACGGCTGAAGAAAAGCCCTCG 32) CCGCGGCGGTCGCTGTCTCAGCCGTTGCCTCCGCGGCCGT CGCCGGCCGCCCTTCCCGGCGGCGAAGTCTCGGGGAAAGG CCCAGCGGTGGCAGCCCGAGAGGCTCGCGACCCTCTCCCG GACGCCGGGGCCTCGCCGGCACCTAGCCGCTGCTGCCGCC GCCGTTCCTCCGTGGCCTTTTTCGCCGTGTGCGACGGGCA CGGCGGGCGGGAGGCGGCACAGTTTGCCCGGGAGCACTTG TGGGGTTTCATCAAGAAGCAGAAGGGTTTCACCTCGTCCG AGCCGGCTAAGGTTTGCGCTGCCATCCGCAAAGGCTTTCT CGCTTGTCACCTTGCCATGTGGAAGAAACTGGCGGAATGG CCAAAGACTATGACGGGTCTTCCTAGCACATCAGGGACAA CTGCCAGTGTGGTCATCATTCGGGGCATGAAGATGTATGT AGCTCACGTAGGTGACTCAGGGGTGGTTCTTGGAATTCAG GATGACCCGAAGGATGACTTTGTCAGAGCTGTGGAGGTGA CACAGGACCATAAGCCAGAACTTCCCAAGGAAAGAGAACG AATCGAAGGACTTGGTGGGAGTGTAATGAACAAGTCTGGG GTGAATCGTGTAGTTTGGAAACGACCTCGACTCACTCACA ATGGACCTGTTAGAAGGAGCACAGTTATTGACCAGATTCC TTTTCTGGCAGTAGCAAGAGCACTTGGTGATTTGTGGAGC TATGATTTCTTCAGTGGTGAATTTGTGGTGTCACCTGAAC CAGACACAAGTGTCCACACTCTTGACCCTCAGAAGCACAA GTATATTATATTGGGGAGTGATGGACTTTGGAATATGATT CCACCACAAGATGCCATCTCAATGTGCCAGGACCAAGAGG AGAAAAAATACCTGATGGGTGAGCATGGACAATCTTGTGC CAAAATGCTTGTGAATCGAGCATTGGGCCGCTGGAGGCAG CGTATGCTCCGAGCAGATAACACTAGTGCCATAGTAATCT GCATCTCTCCAGAAGTGGACAATCAGGGAAACTTTACCAA TGAAGATGAGTTATACCTGAACCTGACTGACAGCCCTTCC TATAATAGTCAAGAAACCTGTGTGATGACTCCTTCCCCAT GTTCTACACCACCAGTCAAGTCACTGGAGGAGGATCCATG GCCAAGGGTGAATTCTAAGGACCATATACCTGCCCTGGTT CGTAGCAATGCCTTCTCAGAGAATTTTTTAGAGGTTTCAG CTGAGATAGCTCGAGAGAATGTCCAAGGTGTAGTCATACC CTCAAAAGATCCAGAACCACTTGAAGAAAATTGCGCTAAA GCCCTGACTTTAAGGATACATGATTCTTTGAATAATAGCC TTCCAATTGGCCTTGTGCCTACTAATTCAACAAACACTGT CATGGACCAAAAAAATTTGAAGATGTCAACTCCTGGCCAA ATGAAAGCCCAAGAAATTGAAAGAACCCCTCCAACAAACT TTAAAAGGACATTAGAAGAGTCCAATTCTGGCCCCCTGAT GAAGAAGCATAGACGAAATGGCTTAAGTCGAAGTAGTGGT GCTCAGCCTGCAAGTCTCCCCACAACCTCACAGCGAAAGA ACTCTGTTAAACTCACCATGCGACGCAGACTTAGGGGCCA GAAGAAAATTGGAAATCCTTTACTTCATCAACACAGGAAA ACTGTTTGTGTTTGCTGA Trunc1 ATGGCGGGGCTGTACTCGCTGGGAGTGAGCGTCTTCTCCG (SEQ ACCAGGGCGGGAGGAAGTACATGGAGGACGTTACTCAAAT ID NO: CGTTGTGGAGCCCGAACCGACGGCTGAAGAAAAGCCCTCG 33) CCGCGGCGGTCGCTGTCTCAGCCGTTGCCTCCGCGGCCGT CGCCGGCCGCCCTTCCCGGCGGCGAAGTCTCGGGGAAAGG CCCAGCGGTGGCAGCCCGAGAGGCTCGCGACCCTCTCCCG GACGCCGGGGCCTCGCCGGCACCTAGCCGCTGCTGCCGCC GCCGTTCCTCCGTGGCCTTTTTCGCCGTGTGCGACGGGCA CGGCGGGCGGGAGGCGGCACAGTTTGCCCGGGAGCACTTG TGGGGTTTCATCAAGAAGCAGAAGGGTTTCACCTCGTCCG AGCCGGCTAAGGTTTGCGCTGCCATCCGCAAAGGCTTTCT CGCTTGTCACCTTGCCATGTGGAAGAAACTGGCGGAATGG CCAAAGACTATGACGGGTCTTCCTAGCACATCAGGGACAA CTGCCAGTGTGGTCATCATTCGGGGCATGAAGATGTATGT AGCTCACGTAGGTGACTCAGGGGTGGTTCTTGGAATTCAG GATGACCCGAAGGATGACTTTGTCAGAGCTGTGGAGGTGA CACAGGACCATAAGCCAGAACTTCCCAAGGAAAGAGAACG AATCGAAGGACTTGGTGGGAGTGTAATGAACAAGTCTGGG GTGAATCGTGTAGTTTGGAAACGACCTCGACTCACTCACA ATGGACCTGTTAGAAGGAGCACAGTTATTGACCAGATTCC TTTTCTGGCAGTAGCAAGAGCACTTGGTGATTTGTGGAGC TATGATTTCTTCAGTGGTGAATTTGTGGTGTCACCTGAAC CAGACACAAGTGTCCACACTCTTGACCCTCAGAAGCACAA GTATATTATATTGGGGAGTGATGGACTTTGGAATATGATT CCACCACAAGATGCCATCTCAATGTGCCAGGACCAAGAGG AGAAAAAATACCTGATGGGTGAGCATGGACAATCTTGTGC CAAAATGCTTGTGAATCGAGCATTGGGCCGCTGGAGGCAG CGTATGCTCCGAGCAGATAACACTAGTGCCATAGTAATCT GCATCTCTCCAGAAGTGGACAATCAGGGAAACTTTACCAA TGAAGATGAGTTATACCTGAACCTGACTGACAGCCCTTCC TATAATAGTCAAGAAACCTGTGTGATGACTCCTTCCCCAT GTTCTACACCACCAGTCAAGTCACTGGAGGAGGATCCATG GCCAAGGGTGAATTCTAAGGACCATATACCTGCCCTGGTT CGTAGCAATGCCTTCTCAGAGAATTTTTTAGAGGTTTCAG CTGAGATAGCTCGAGAGAATGTCCAAGGTGTAGTCATACC CTCAAAAGATCCAGAACCACTTGAAGAAAATTGCTAA Trunc2 ATGGCGGGGCTGTACTCGCTGGGAGTGAGCGTCTTCTCCG (SEQ ACCAGGGCGGGAGGAAGTACATGGAGGACGTTACTCAAAT ID NO: CGTTGTGGAGCCCGAACCGACGGCTGAAGAAAAGCCCTCG 34) CCGCGGCGGTCGCTGTCTCAGCCGTTGCCTCCGCGGCCGT CGCCGGCCGCCCTTCCCGGCGGCGAAGTCTCGGGGAAAGG CCCAGCGGTGGCAGCCCGAGAGGCTCGCGACCCTCTCCCG GACGCCGGGGCCTCGCCGGCACCTAGCCGCTGCTGCCGCC GCCGTTCCTCCGTGGCCTTTTTCGCCGTGTGCGACGGGCA CGGCGGGCGGGAGGCGGCACAGTTTGCCCGGGAGCACTTG TGGGGTTTCATCAAGAAGCAGAAGGGTTTCACCTCGTCCG AGCCGGCTAAGGTTTGCGCTGCCATCCGCAAAGGCTTTCT CGCTTGTCACCTTGCCATGTGGAAGAAACTGGCGGAATGG CCAAAGACTATGACGGGTCTTCCTAGCACATCAGGGACAA CTGCCAGTGTGGTCATCATTCGGGGCATGAAGATGTATGT AGCTCACGTAGGTGACTCAGGGGTGGTTCTTGGAATTCAG GATGACCCGAAGGATGACTTTGTCAGAGCTGTGGAGGTGA CACAGGACCATAAGCCAGAACTTCCCAAGGAAAGAGAACG AATCGAAGGACTTGGTGGGAGTGTAATGAACAAGTCTGGG GTGAATCGTGTAGTTTGGAAACGACCTCGACTCACTCACA ATGGACCTGTTAGAAGGAGCACAGTTATTGACCAGATTCC TTTTCTGGCAGTAGCAAGAGCACTTGGTGATTTGTGGAGC TATGATTTCTTCAGTGGTGAATTTGTGGTGTCACCTGAAC CAGACACAAGTGTCCACACTCTTGACCCTCAGAAGCACAA GTATATTATATTGGGGAGTGATGGACTTTGGAATATGATT CCACCACAAGATGCCATCTCAATGTGCCAGGACCAAGAGG AGAAAAAATACCTGATGGGTGAGCATGGACAATCTTGTGC CAAAATGCTTGTGAATCGAGCATTGGGCCGCTGGAGGCAG CGTATGCTCCGAGCAGATAACACTAGTGCCATAGTAATCT GCATCTCTCCAGAAGTGGACAATCAGGGAAACTTTACCAA TGAAGATGAGTTATACCTGAACCTGACTGACAGCCCTTCC TATAATAGTCAAGAAACCTGTGTGATGACTCCTTCCCCAT GTTCTACACCACCAGTCAAGTCACTGGAGGAGGATCCATG GCCAAGGGTGAATTCTAAGGACCATATACCTGCCCTGGTT CGTAGCAATGCCTTCTCAGAGAATTTTTTAGAGGTTTCAG CTGAGATAGCTCGAGAGAATGTCCAAGGTGTAGTCATACC CTCAAAAGATCCAGAACCACTTGAATGA C- CGAAATGGCTTAAGTCGAAGTAGTGGTGCTCAGCCTGCAA term- GTCTCCCCACAACCTCACAGCGAAAGAACTCTGTTAAACT inal CACCATGCGACGCAGACTTAGGGGCCAGAAGAAAATTGGA (SEQ AATCCTTTACTTCATCAACACAGGAAAACTGTTTGTGTTT ID NO: GCTGA 35)

The fluorescence level of mCherry, which is expressed following an IRES sequence, provided an internal control for vector expression in each cell. Using this system, it was found that the PPM1D truncation mutations increased the GFP/mCherry ratio, indicating a relative decrease in degradation of truncated PPM1D (FIG. 8C), consistent with Western blots of the truncated protein (FIG. 2B). In contrast, the GFP/mCherry ratio in cells expressing the C-terminal region of PPM1D was decreased, indicating the presence of a degradation signal in this region (FIG. 8C). The GFP/mCherry ratios did not differ between Molm13 p53 wild type and Molm13 p53^(−/−) cells (FIG. 8D). Without being bound by theory this demonstrated that, while PPM1D gene expression is regulated by p53, the degradation of PPM1D is p53-independent. Treatment with the proteasome-inhibitor MG132 led to decreased degradation of wild-type and C-terminal PPM1D, but not of the truncating mutants (FIG. 8E). These data demonstrate that the C-terminal domain of PPM1D contains a degradation signal that is deleted by PPM1D exon 6 truncation mutations, leading to decreased proteosomal degradation and consequent overexpression of PPM1D.

Whether overexpression of PPM1D is sufficient to induce chemotherapy resistance, or whether a novel function of the truncated protein is required for this phenotype was examined. Full length PPM1D was over-expressed in Molm13 cells and these cells were exposed to cytarabine. A similar degree of chemotherapy resistance was observed in PPM1D-mutant cells and cells with overexpression of wild type PPM1D (FIG. 8F). Thus, PPM1D overexpression, as occurs due to C-terminal deletions, was sufficient to induce chemotherapy resistance.

Example 4: Mutations in PPM1D Abrogate the DNA Damage Response to Genotoxic Therapy

PPM1D directly regulates TP53 and other components of the DNA damage response pathway through its protein phosphatase activity (Fiscella et al. Proc. Natl. Acad. Sci. U.S.A. 94, 6048-53 (1997); Lu, X. et al. Cell Cycle 4, 4060-4064 (2005); Fujimoto, H. et al. Cell Death Differ. 13, 1170-80 (2006); Takekawa, M. et al. EMBO J. 19, 6517-26 (2000); Lu, X. et al. Cancer Metastasis Rev. 27, 123-35 (2008); Lu, X. et al. Genes Dev. 19, 1162-74 (2005)). Whether PPM1D mutations abrogate the p53-dependent DNA damage response pathway in leukemia cells was examined. The genotoxic effects of chemotherapy elicit a strong DNA damage response (DDR), which among others includes the phosphorylation of Chk1 and p53. PPM1D is best known for its role as a negative regulator of this response, leading to dephosphorylation of these targets. In view of the gain of function induced by truncating PPM1D mutations, the effects of truncating PPM1D mutations on the response to chemotherapy treatment were studied. Molm13 PPM1D mutant and wild type control cells were exposed to Cytarabine treatment. Cytarabine induced phosphorylation of known PPM1D targets (Lu, X. et al. Genes Dev. 19, 1162-74 (2005)), p53 Ser15 and Chk1 Ser345, in control leukemia cells, but this response was abrogated in PPM1D-mutant cells (FIG. 9A). Moreover, PPM1D mutation decreased apoptosis as assessed by Annexin V staining (FIG. 9B) and increased progression to G2/M phase compared to control cells following exposure to chemotherapy (FIG. 9C).

To explore the spectrum of PPM1D targets in hematopoietic cells, a quantitative phosphoproteomic analysis was performed in PPM1D wild-type and mutant cells at baseline and in response to chemotherapy. Altered phosphorylation of many components of the full DNA damage response pathway was observed in PPM1D-mutant leukemia cells (FIG. 9D), including differential phosphorylation of TP53, PPM1D, CHEK1, CHEK2 and MDM4 (Lu, X. et al. Cancer Metastasis Rev. 27, 123-35 (2008); Lu, X. et al. Genes Dev. 19, 1162-74 (2005); Zhang, X. et al. Cancer Res. 69, 7960-8 (2009)). In addition, CDKN1A (p21) was identified as a new DNA damage response target of PPM1D. Based on the peptides with altered phosphorylation in PPM1D-mutant cells, a consensus sequence was identified for the serine-threonine phosphatase activity of PPM1D (FIGS. 9E and 9F). Because many phosphorylation sites are not located on peptides that are detected by mass spectrometry, the consensus sequence was used to predict additional PPM1D targets. Known PPM1D targets, including TP53, CHEK1, CHEK2, ATM, ATR and MDM2, bear the consensus target sequence. In addition, new phosphorylation sites were identified in components of the DNA damage response pathway that are predicted targets of PPM1D based on the consensus sequence. Without being bound by theory, these data demonstrate the central role of PPM1D in the DNA damage pathway (FIG. 9G), and demonstrate the full extent to which PPM1D mutation in leukemia cells alter this pathway.

Because C-terminal PPM1D mutations lead to increased protein expression, it was tested whether inhibition of PPM1D could reverse the aberrant phosphorylation pattern observed in PPM1D-mutant cells. An allosteric PPM1D inhibitor, GKS2830371, has previously been shown to be highly selective for the PPM1D phosphatase (Gilmartin, A. G. et al. Nat. Chem. Biol. 10, 181-7 (2014)). Treatment with GKS2830371 increased p53 Ser15 phosphorylation, an established PPM1D target, in Molm13 PPM1D-mutant cells following cytarabine treatment (FIG. 10A). Using phosphoproteomic analysis, it was found that the addition of low-dose GSK2830371 to cytarabine treatment led to a complete reversal of the aberrant phosphorylation pattern observed in PPM1D-mutant cells in response to chemotherapy (FIG. 10B).

Whether treatment with GSK2830371 could reverse the chemotherapy resistance induced by PPM1D mutation was examined. Combined treatment with cytarabine and GSK2830371 increased the sensitivity of Molm13 PPM1D-mutant cells to cytarabine (FIG. 10C). In addition, the competitive advantage of Molm13 PPM1D-mutant cells in cytarabine-exposed cells could be reversed through the addition of GSK2830371 treatment (FIG. 10D). Moreover, it was found that Molm13 PPM1D-mutant cells had an increased sensitivity to single agent PPM1D inhibitor treatment when compared to control cells, as assessed by cell viability analysis (FIG. 10E) and Annexin V staining (FIG. 10F). These data indicate that PPM1D inhibition can re-sensitize PPM1D-mutant cells to chemotherapy treatment, and is beneficial for the targeted elimination of PPM1D-mutant cells.

Truncating mutations of PPM1D lead to gain of function of the protein, resulting in resistance to DNA damaging therapy. It was therefore determined whether inhibition of the protein could sensitize PPM1D mutant cells to chemotherapy treatment. To test the response of PPM1D mutant and wild type cells to PPM1D inhibition, the cells were exposed to increasing drug concentrations of two commercially available PPM1D inhibitors (GSK2830371 and CCT007093), that work through different mechanisms (Gilmartin, A. G. et al. Nat. Chem. Biol. 10, 181-7 (2014); Rayter S et al. Oncogene. 27, 1036-1044 (2008)). As shown by a 72-hour cell viability assay, PPM1D mutant cells have an increased sensitivity to PPM1D inhibition with either compound in comparison to wild type control cells (FIGS. 11A and 11B). The addition of a PPM1D inhibitor sensitized PPM1D mutant cells to treatment with Cytarabine in a dose dependent manner In line with these results, treatment with the PPM1D inhibitor caused a dose dependent upregulation of phospo p53 (Ser15), thereby reversing the abrogated DDR response characteristic of PPM1D mutant cells (FIG. 10D).

Collectively, these results demonstrate that PPM1D mutations confer a competitive advantage to hematopoietic cells undergoing genotoxic stress through an extensive abrogation of the DNA damage response pathway. These findings provide evidence for a model in which HSPCs carrying PPM1D mutations selectively expand during chemotherapy treatment, providing the initiating mutation in a large proportion of therapy-related myeloid neoplasms. This model is consistent with reports of PPM1D mutations in the peripheral blood of cancer patients having received chemotherapy, and with the enrichment of PPM1D and TP53 mutations in therapy-related MDS (Lindsley, R. C. et al. N. Engl. J. Med. 376, 536-547 (2017)). TP53 mutations have also been found to expand during chemotherapy treatment and to be associated with therapy-related myeloid neoplasms (Wong, T. et al. Nature 518, 552-555 (2015)). However, while TP53 mutations are characterized by a complex karyotype, PPM1D mutations are not, demonstrating that the biology and clinical phenotype associated with PPM1D mutations is distinct from p53 inactivation (Lindsley, R. C. et al. N. Engl. J. Med. 376, 536-547 (2017)). The phosphoproteomic data described herein support this rationale, as PPM1D mutations were found to inhibit the full DNA damage response pathway rather than merely inhibiting p53.

In addition to providing a model for the selective advantage of PPM1D-mutant HSPCs in the presence of chemotherapy, it was demonstrated that PPM1D mutations cause a gain-of-function through increased PPM1D protein expression that is responsive to targeted treatment with a PPM1D inhibitor, highlighting several potential therapeutic opportunities. Chemotherapy treatment can result in the development of therapy-related myeloid neoplasms (also termed “t-MNs”), which are characterized by chemotherapy resistance and a poor prognosis (Morton, L. M. et al. Blood 121, 2996-3004 (2013); Malmgren, J., et al. Leukemia Res 47, 178-184 (2016); Candelaria, M. and Dueñas-Gonzalez, A. Expert Opin Drug Saf 14, 655-65 (2015)). Recent studies have demonstrated that truncating mutations of the protein phosphatase Mg2⁺/Mn2⁺ 1D (PPM1D) were detected in the blood of healthy people (Jaiswal, S. et al. N. Engl. J. Med. 371, 2488-98 (2014); Genovese, G. et al. N. Engl. J. Med. 371, 2477-87 (2014); Xie, M. et al. Nat. Med. 20, 1472-8 (2014)), as well as in up to 25% of solid tumor cancer patients exposed to chemotherapy (Ruark, E. et al. Nature 493, 406-10 (2013); Zajkowicz, A. et al. Br. J. Cancer 112, 1114-20 (2015); Akbari, M. R. et al. J. Natl. Cancer Inst. 106, djt323 (2014); Pharoah, P. D. et al. J. Natl. Cancer Inst. 108, (2016); Swisher, E. M. et al. JAMA Oncol (2016)). Additionally, PPM1D mutations were recently found to occur in myelodysplastic syndromes (MDS) and to be enriched in therapy-related MDS, where they are present in 15% of cases (Lindsley, R. C. et al. N. Engl. J. Med. 376, 536-547 (2017)).

As described herein, truncating PPM1D mutations conferred chemotherapy resistance through an abrogation of the DNA damage response. This leads to a competitive advantage of PPM1D-mutant cells and induces selective outgrowth of PPM1D-mutant hematopoietic stem and progenitor cells (HSPCs) during chemotherapy exposure in vivo. Through quantitative phosphoproteomic analysis, a consensus target sequence for PPM1D was identified. It was demonstrated that PPM1D targets the full DNA damage response pathway in hematopoietic cells, and that truncating PPM1D mutations cause a gain-of-function through loss of a C-terminal degradation signal. Treatment with an allosteric PPM1D inhibitor, GSK2830371 (Gilmartin, A. G. et al. Nat. Chem. Biol. 10, 181-7 (2014)), reverses the chemotherapy resistance phenotype and selectively kills PPM1D-mutant cells. In addition to providing an explanation for the high frequency of PPM1D mutations in chemotherapy treated patients and therapy-related myeloid neoplasms, these findings have the potential to open up a new therapeutic avenue for the targeted treatment of chemotherapy resistant, PPM1D-mutant therapy-related myeloid neoplasms which are known to have a poor prognosis. PPM1D inhibitor therapy could be employed to prevent the emergence of PPM1D-mutant CHIP clones. Similarly, PPM1D inhibitor treatment might be used to inhibit chemotherapy-induced outgrowth of PPM1D-mutant hematopoietic stem cells, potentially decreasing the likelihood of future development of therapy-related myeloid neoplasms (t-MNs). Finally, PPM1D inhibition may be used as a therapy for t-MN, highly lethal diseases that are resistant to chemotherapy and in great need of new treatment options. Thus, these data provide a rationale for preventative cancer care, through which t-MN development can be prevented by adjuvant depletion of PPM1D-mutant cells.

Other Embodiments

From the foregoing description, it will be apparent that variations and modifications may be made to the invention described herein to adopt it to various usages and conditions. Such embodiments are also within the scope of the following claims.

The recitation of a listing of elements in any definition of a variable herein includes definitions of that variable as any single element or combination (or subcombination) of listed elements. The recitation of an embodiment herein includes that embodiment as any single embodiment or in combination with any other embodiments or portions thereof.

All patents and publications mentioned in this specification are herein incorporated by reference to the same extent as if each independent patent and publication was specifically and individually indicated to be incorporated by reference. 

What is claimed is:
 1. A method of increasing sensitivity or reversing resistance of a blood or hematologic cancer cell to a chemotherapeutic agent or inhibiting proliferation of a blood or hematologic cancer cell, the method comprising contacting the blood or hematologic cancer cell which is or has become resistant to a chemotherapeutic agent with an effective amount of a Protein phosphatase 1D (PPM1D) inhibitor, thereby increasing sensitivity or reversing resistance of the blood or hematologic cancer cell to the chemotherapeutic agent, or inhibiting proliferation.
 2. The method of claim 1, wherein the blood or hematologic cancer cell is in a subject having a blood or hematologic cancer.
 3. The method of claim 2, wherein the method treats the blood or hematologic cancer in the subject.
 4. The method of claim 1, wherein the blood or hematologic cancer cell is in vivo or in vitro.
 5. The method of claim 1, wherein the PPM1D inhibitor is selected from the group consisting of GSK2830371, CCT007093, and analogs thereof.
 6. The method of claim 1, wherein the chemotherapeutic agent is a DNA damaging agent selected from the group consisting of Cytarabine, Doxorubicin, Cyclophosphamide, and Cisplatin.
 7. The method of claim 1, wherein the PPM1D inhibitor inhibits the activity of a PPM1D polypeptide comprising a truncation mutation and/or a gain-of-function mutation.
 8. The method of claim 2, wherein the blood or hematologic cancer cell is a hematologic cancer cell.
 9. The method of claim 2, wherein the blood or hematologic cancer cell is a therapy-related myeloid neoplasm.
 10. The method of claim 2, wherein the blood or hematologic cancer cell is derived from blood, bone marrow or a tumor sample. 